Looking for modules in Proliferating CD4

Much of the opioid literature suggests that proliferating CD4 are responsible for a large part of the opioid dependent CD4 impact. Objective here is to try and identify those modules. See module RMD for more of the intuition/logic as to choices made.

Possible comparisons

There are many iterations we could select for this analysis, from most ideal to least ideal: * Participant + Treatment + Timepoint * Treatment + Timepoint * Participant + Treatment * Treatment

Which can further be expanded to which CD4 populations are included. A more robust CD4 module ID will occur at a later point. First we just subset proliferating cells, then we get the parts of those that are in each subset.

results<-subset(results, idents = "Proliferating")
## Loading required package: Signac
table(results$Treatment)
## 
##   Bup.Nalo  Methadone Naltrexone 
##        330         56        138
table(results$Timepoint)
## 
##   0   3 
## 197 327
table(paste(results$Treatment, results$Timepoint))
## 
##   Bup.Nalo 0   Bup.Nalo 3  Methadone 0  Methadone 3 Naltrexone 0 Naltrexone 3 
##          101          229           13           43           83           55
table(paste(results$Treatment, results$Participant))
## 
##   Bup.Nalo 5014   Bup.Nalo 5017   Bup.Nalo 5018   Bup.Nalo 5023  Methadone 5003 
##              42             145             133              10              10 
##  Methadone 5009  Methadone 5016  Methadone 5020 Naltrexone 5021 Naltrexone 5026 
##              22              11              13               7              59 
## Naltrexone 5035 Naltrexone 5037 
##              17              55
table(paste(results$Treatment, results$Timepoint, results$Participant))
## 
##   Bup.Nalo 0 5014   Bup.Nalo 0 5017   Bup.Nalo 0 5018   Bup.Nalo 0 5023 
##                 7                37                54                 3 
##   Bup.Nalo 3 5014   Bup.Nalo 3 5017   Bup.Nalo 3 5018   Bup.Nalo 3 5023 
##                35               108                79                 7 
##  Methadone 0 5003  Methadone 0 5009  Methadone 0 5016  Methadone 0 5020 
##                 4                 1                 4                 4 
##  Methadone 3 5003  Methadone 3 5009  Methadone 3 5016  Methadone 3 5020 
##                 6                21                 7                 9 
## Naltrexone 0 5021 Naltrexone 0 5026 Naltrexone 0 5035 Naltrexone 0 5037 
##                 3                33                 8                39 
## Naltrexone 3 5021 Naltrexone 3 5026 Naltrexone 3 5035 Naltrexone 3 5037 
##                 4                26                 9                16

We need “enough” cells to have a hope of identifying modules. “Enough” is a hard call, but in my experience, around 50 cells are needed to call a module. Clearly the most desirable (treatment, timepoint, and participant specific) is not sufficient to call modules. Treatment + pariticipant also has too few cells in the methadone and Naltrexone groups to ID modules. Treatment timepoint is borderline for all except methadone time 0, but seems close enough to try at least. Timepoint and treatment alone both have sufficient cells, and we can try to call modules with them.

results$T_TP<-paste(results$Treatment, results$Timepoint, sep="_")

results.split<-SplitObject(results, "T_TP")
#npcs and softpowers, selecting npc based on last nonplataue pc on elbow plot, selecting softpower as first above 0.8 
#nothing for methadone, PCA doesnt have enough observations, go modules for the other two 
conds<-cbind(c(7,6, 7, 9,1,1),c(5,9, 8, 14,1,1 ))
mods1<-WrapGroupModID(results.split, "NA", conds)
## [1] "Bup.Nalo_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.3816
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.49885
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.207e-15
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1 
## Positive:  RRM2, DIAPH3, POLQ, NCAPG, HIST1H1B, SMC2, TOP2A, NCAPG2, MKI67, NUSAP1 
##     SHCBP1, CENPP, FBXO5, FANCI, ASPM, ATAD5, KIF15, KNL1, TUBB, TUBA1B 
## Negative:  LTB, XIST, ANK3, TTN, JUNB, FMN1, AP000787.1, MPP7, LINC01934, ZNF331 
##     AC105402.3, MAML2, SESN3, DPYD-AS1, UST, TOX, FAAH2, JUN, FAM13A, DUSP2 
## PC_ 2 
## Positive:  RPTOR, SLFN12L, MGAT5, UTY, MTAP, CASK, POLQ, KIF18B, ATAD5, HIVEP1 
##     KNTC1, CIT, WWOX, ZNF236, SNX29, BTBD11, FANCD2, PITPNC1, POLE, RAP1GAP2 
## Negative:  RPS2, RPL41, RPL28, RPS15, RPL27A, RPS18, RPL18A, PFN1, RPLP1, RPL13A 
##     RPS16, RPS12, TMSB4X, RPL18, RPS19, GAPDH, TMSB10, RPS23, RPS28, RPS27 
## PC_ 3 
## Positive:  PLK1, KIF14, HMMR, PIF1, CDCA2, SGO2, CCNB1, INCENP, KIF20A, AURKA 
##     UBE2C, KIF2C, KIF4A, CCNB2, KPNA2, SPDL1, TOP2A, ASPM, KIF18B, KIF23 
## Negative:  MIR4422HG, PECAM1, DTHD1, MCTP2, GZMK, LYST, PTPN3, NCOA1, MYB, PON2 
##     HAVCR2, SESTD1, CD38, SAMD3, LRMP, AL031599.1, PACSIN1, POU2AF1, DNAJC1, TRPS1 
## PC_ 4 
## Positive:  MIR4422HG, PECAM1, PTPN3, GZMK, LYST, MCTP2, NKG7, DTHD1, KPNA2, AGAP1 
##     AL031599.1, FXYD2, LRMP, CBLB, UBE2E2, SESTD1, HAVCR2, CENPF, PTPRE, KIF20A 
## Negative:  AKT3, FKBP5, MSH6, SSBP2, SCFD2, MPP6, LTB, FANCA, GPHN, CDC6 
##     PUS7, ORC6, TANC2, SNED1, DISC1, RBBP8, DTL, CDC45, FAM111B, CCNE2 
## PC_ 5 
## Positive:  KCNQ5, AGAP1, E2F7, CCNE2, HIST1H1D, AFF3, XIST, PECAM1, C1orf21, SKA3 
##     KLRK1, HIST1H3D, GZMK, RFC3, HIST1H2BM, CSRP3-AS1, CDCA5, CD8B, CREB5, NEIL3 
## Negative:  PLCL1, MGAT5, RORA, NEAT1, AL136456.1, UTY, CDHR3, ABLIM1, LINC02384, IQGAP2 
##     CLIC5, CD59, IL6R, LGMN, IL2RA, SGO1-AS1, LINC00278, MAST4, MRPL33, MTERF1 
##    Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1      1   0.0298  1.71         0.5850 148.000  1.46e+02 166.00
## 2      2   0.4170 -2.69         0.6070  79.800  7.74e+01 103.00
## 3      3   0.6290 -2.44         0.7540  44.200  4.18e+01  67.20
## 4      4   0.7880 -2.26         0.8790  25.300  2.27e+01  46.20
## 5      5   0.8600 -2.04         0.8770  15.000  1.25e+01  33.30
## 6      6   0.8170 -1.95         0.7980   9.190  7.01e+00  24.80
## 7      7   0.8540 -1.76         0.8290   5.870  3.98e+00  19.10
## 8      8   0.7580 -1.73         0.7100   3.890  2.27e+00  15.00
## 9      9   0.7750 -1.62         0.7440   2.670  1.33e+00  12.00
## 10    10   0.2290 -3.22         0.1260   1.890  7.84e-01   9.79
## 11    12   0.8820 -1.34         0.9150   1.030  2.86e-01   6.69
## 12    14   0.8360 -1.24         0.8620   0.606  1.18e-01   4.72
## 13    16   0.2010 -2.15         0.0357   0.378  4.94e-02   3.42
## 14    18   0.2100 -2.06         0.0432   0.245  2.15e-02   2.51
## 15    20   0.8700 -1.22         0.9110   0.163  9.63e-03   1.88

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##  0  1  2  3  4  5  6  7  8  9 10 
##  9 72 47 36 24 24 20 13 13 13 12

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 11 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 8 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 8 module eigengenes in given set.
## $blue
##   [1] "RRM2"       "DIAPH3"     "POLQ"       "NCAPG"      "HIST1H1B"  
##   [6] "SMC2"       "TOP2A"      "NCAPG2"     "MKI67"      "NUSAP1"    
##  [11] "SHCBP1"     "CENPP"      "FBXO5"      "FANCI"      "ASPM"      
##  [16] "ATAD5"      "KIF15"      "KNL1"       "TUBB"       "TUBA1B"    
##  [21] "TMPO"       "DTL"        "SPC25"      "STMN1"      "CIT"       
##  [26] "AL136456.1" "RPTOR"      "SLFN12L"    "MGAT5"      "UTY"       
##  [31] "MTAP"       "KIF18B"     "HIVEP1"     "KNTC1"      "WWOX"      
##  [36] "ZNF236"     "SNX29"      "BTBD11"     "FANCD2"     "POLE"      
##  [41] "RAP1GAP2"   "RBL1"       "RORA"       "WDHD1"      "PCNT"      
##  [46] "IQGAP2"     "PLK1"       "KIF14"      "HMMR"       "PIF1"      
##  [51] "CDCA2"      "SGO2"       "CCNB1"      "INCENP"     "KIF20A"    
##  [56] "AURKA"      "UBE2C"      "KIF2C"      "KIF4A"      "CCNB2"     
##  [61] "KPNA2"      "SPDL1"      "KIF23"      "CCNF"       "ESPL1"     
##  [66] "CDCA8"      "CKAP2L"     "DEPDC1B"    "MYB"        "SAMD3"     
##  [71] "CENPF"      "MSH6"       "SSBP2"      "SCFD2"      "MPP6"      
##  [76] "FANCA"      "GPHN"       "CDC6"       "PUS7"       "ORC6"      
##  [81] "TANC2"      "RBBP8"      "CDC45"      "FAM111B"    "CCNE2"     
##  [86] "USP37"      "WDR76"      "HELLS"      "E2F7"       "HIST1H1D"  
##  [91] "SKA3"       "HIST1H3D"   "RFC3"       "HIST1H2BM"  "CDCA5"     
##  [96] "NEIL3"      "UHRF1"      "MCM10"      "RAD51AP1"   "PLCL1"     
## [101] "NEAT1"      "CDHR3"      "ABLIM1"     "LINC02384"  "CLIC5"     
## [106] "CD59"       "IL6R"       "LGMN"       "IL2RA"      "SGO1-AS1"  
## [111] "LINC00278"  "MAST4"      "MTERF1"     "ADD3-AS1"   "TEX9"      
## [116] "GPR15"      "RFX3-AS1"   "RFX3"       "ZRANB3"     "PPP3CA"    
## [121] "HSP90AA1"   "AGPAT4"     "KHDC1"      "SYTL2"      "TNFRSF1B"  
## [126] "CLSPN"      "HMGB1"      "BIRC5"      "DNMT1"      "AUTS2"     
## [131] "TPM4"       "TXK"        "PRKCA"      "SELL"       "HIST1H2BK" 
## [136] "BACH2"      "XYLB"       "MCM5"       "PXMP2"      "IGF1R"     
## [141] "PLAGL1"     "DMC1"       "F5"        
## 
## $purple
##  [1] "LTB"        "ANK3"       "JUNB"       "FMN1"       "AP000787.1"
##  [6] "MPP7"       "ZNF331"     "SESN3"      "DPYD-AS1"   "SPON1"     
## [11] "SNED1"      "FHIT"      
## 
## $black
##  [1] "XIST"       "TTN"        "TOX"        "FAM13A"     "CCDC141"   
##  [6] "CDK14"      "AC093865.1" "CPM"        "RBMS3"      "IKZF2"     
## [11] "MAGI1"      "MIR181A1HG" "ST8SIA1"   
## 
## $magenta
##  [1] "LINC01934"   "UST"         "MCF2L2"      "MRPL33"      "TRERF1"     
##  [6] "MSC-AS1"     "AC104073.4"  "IQCJ-SCHIP1" "CTSW"        "RBPJ"       
## [11] "BFSP1"       "LINC02694"   "HOPX"       
## 
## $brown
##  [1] "DUSP2"   "RPS2"    "RPL41"   "RPL28"   "RPS15"   "RPL27A"  "RPS18"  
##  [8] "RPL18A"  "PFN1"    "RPLP1"   "RPL13A"  "RPS16"   "RPS12"   "TMSB4X" 
## [15] "RPL18"   "RPS19"   "GAPDH"   "TMSB10"  "RPS23"   "RPS28"   "RPS27"  
## [22] "RPLP2"   "RPL37"   "RPS4X"   "RPL37A"  "RPL11"   "C1orf21" "CALM1"  
## [29] "IL18RAP" "ATP5F1E" "ANXA1"   "ENO1"    "CORO1A"  "SMIM20"  "MAP3K8" 
## [36] "RPS6"   
## 
## $red
##  [1] "AFF3"       "CASK"       "PITPNC1"    "MIR4422HG"  "PECAM1"    
##  [6] "DTHD1"      "MCTP2"      "GZMK"       "LYST"       "PTPN3"     
## [11] "NCOA1"      "PON2"       "HAVCR2"     "SESTD1"     "CD38"      
## [16] "LRMP"       "AL031599.1" "PACSIN1"    "POU2AF1"    "DNAJC1"    
## [21] "TRPS1"      "GTDC1"      "IL19"       "AGAP1"      "LGALS3"    
## [26] "ZSWIM6"     "FXYD2"      "CBLB"       "UBE2E2"     "PTPRE"     
## [31] "TNIP3"      "AL603840.1" "KCNQ5"      "KLRK1"      "CSRP3-AS1" 
## [36] "CREB5"      "PAM"        "LINC02614"  "PRELID2"    "SRGAP2B"   
## [41] "TRAV19"     "MTRNR2L8"   "ABCB1"      "NEDD4L"    
## 
## $pink
##  [1] "NKG7"     "CD8B"     "CCL5"     "TGFBR3"   "ZEB2"     "HLA-DPA1"
##  [7] "HLA-DRB1" "HLA-DRB5" "GZMA"     "GAB3"     "MVB12B"   "CD74"    
## [13] "NFIL3"   
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "9588/10000 permutations failed the Mann-Whitney test."
## [1] "9917/10000 permutations failed the Mann-Whitney test."
## [1] "9957/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "8848/10000 permutations failed the Mann-Whitney test."
## [1] "9442/10000 permutations failed the Mann-Whitney test."
## $blue
##   [1] "RRM2"       "DIAPH3"     "POLQ"       "NCAPG"      "HIST1H1B"  
##   [6] "SMC2"       "TOP2A"      "NCAPG2"     "MKI67"      "NUSAP1"    
##  [11] "SHCBP1"     "CENPP"      "FBXO5"      "FANCI"      "ASPM"      
##  [16] "ATAD5"      "KIF15"      "KNL1"       "TUBB"       "TUBA1B"    
##  [21] "TMPO"       "DTL"        "SPC25"      "STMN1"      "CIT"       
##  [26] "AL136456.1" "RPTOR"      "SLFN12L"    "MGAT5"      "UTY"       
##  [31] "MTAP"       "KIF18B"     "HIVEP1"     "KNTC1"      "WWOX"      
##  [36] "ZNF236"     "SNX29"      "BTBD11"     "FANCD2"     "POLE"      
##  [41] "RAP1GAP2"   "RBL1"       "RORA"       "WDHD1"      "PCNT"      
##  [46] "IQGAP2"     "PLK1"       "KIF14"      "HMMR"       "PIF1"      
##  [51] "CDCA2"      "SGO2"       "CCNB1"      "INCENP"     "KIF20A"    
##  [56] "AURKA"      "UBE2C"      "KIF2C"      "KIF4A"      "CCNB2"     
##  [61] "KPNA2"      "SPDL1"      "KIF23"      "CCNF"       "ESPL1"     
##  [66] "CDCA8"      "CKAP2L"     "DEPDC1B"    "MYB"        "SAMD3"     
##  [71] "CENPF"      "MSH6"       "SSBP2"      "SCFD2"      "MPP6"      
##  [76] "FANCA"      "GPHN"       "CDC6"       "PUS7"       "ORC6"      
##  [81] "TANC2"      "RBBP8"      "CDC45"      "FAM111B"    "CCNE2"     
##  [86] "USP37"      "WDR76"      "HELLS"      "E2F7"       "HIST1H1D"  
##  [91] "SKA3"       "HIST1H3D"   "RFC3"       "HIST1H2BM"  "CDCA5"     
##  [96] "NEIL3"      "UHRF1"      "MCM10"      "RAD51AP1"   "PLCL1"     
## [101] "NEAT1"      "CDHR3"      "ABLIM1"     "LINC02384"  "CLIC5"     
## [106] "CD59"       "IL6R"       "LGMN"       "IL2RA"      "SGO1-AS1"  
## [111] "LINC00278"  "MAST4"      "MTERF1"     "ADD3-AS1"   "TEX9"      
## [116] "GPR15"      "RFX3-AS1"   "RFX3"       "ZRANB3"     "PPP3CA"    
## [121] "HSP90AA1"   "AGPAT4"     "KHDC1"      "SYTL2"      "TNFRSF1B"  
## [126] "CLSPN"      "HMGB1"      "BIRC5"      "DNMT1"      "AUTS2"     
## [131] "TPM4"       "TXK"        "PRKCA"      "SELL"       "HIST1H2BK" 
## [136] "BACH2"      "XYLB"       "MCM5"       "PXMP2"      "IGF1R"     
## [141] "PLAGL1"     "DMC1"       "F5"        
## 
## $brown
##  [1] "DUSP2"   "RPS2"    "RPL41"   "RPL28"   "RPS15"   "RPL27A"  "RPS18"  
##  [8] "RPL18A"  "PFN1"    "RPLP1"   "RPL13A"  "RPS16"   "RPS12"   "TMSB4X" 
## [15] "RPL18"   "RPS19"   "GAPDH"   "TMSB10"  "RPS23"   "RPS28"   "RPS27"  
## [22] "RPLP2"   "RPL37"   "RPS4X"   "RPL37A"  "RPL11"   "C1orf21" "CALM1"  
## [29] "IL18RAP" "ATP5F1E" "ANXA1"   "ENO1"    "CORO1A"  "SMIM20"  "MAP3K8" 
## [36] "RPS6"   
## 
## [1] "Bup.Nalo_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.0243
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.49706
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 7.9876e-16
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  PCAT1, FOXP1, ABLIM1, ANK3, C22orf34, INPP5A, SESN3, FAAH2, SCML4, TSHZ2 
##     GMDS-DT, AL136456.1, EXOC6B, FHIT, CCDC18-AS1, PRKCQ, IMMP2L, ATP10A, EHBP1, AC233976.1 
## Negative:  TUBA1B, SLC25A5, TYMS, TUBB, GAPDH, STMN1, PFN1, TPI1, ACTB, PSMA7 
##     HIST1H4C, TK1, RRM2, LDHA, HMGB2, TUBB4B, BIRC5, CLSPN, HNRNPAB, RPSA 
## PC_ 2 
## Positive:  RPL28, B2M, RPL27A, RPL11, RPL10, RPS19, RPS28, RPS12, RPL30, RPL41 
##     RPS23, RPS16, RPS29, RPL13, RPS15A, RPL37A, RPLP1, RPS27, RPS15, RPS18 
## Negative:  KIF18B, SPC25, MELK, CIT, ANLN, POLQ, RAD54L, BRCA2, MKI67, NCAPG2 
##     PLK4, DIAPH3, KIF11, NUSAP1, MASTL, KIF15, CENPE, KNTC1, CCNF, NCAPG 
## PC_ 3 
## Positive:  STAM, KIF14, MAP3K1, IL2RA, CDCA8, KIF4A, KLF2, LTB, CKAP2L, MAF 
##     APOLD1, ESPL1, FOXP1, SESN3, HIST2H2AB, ASPM, RPS3A, CKS1B, ARHGAP11A, TMSB10 
## Negative:  NKG7, KCNQ5, MTHFD1, KLRK1, ZEB2, ARHGAP26, MTHFD1L, SH3RF2, TMEM241, CDC45 
##     CADM1, PRKD3, UNG, FEN1, SLBP, FAM50B, SFMBT2, PECAM1, C1orf21, TIMM13 
## PC_ 4 
## Positive:  FLT1, LINC00665, NOP16, SUPT3H, GNB4, RAB33B, TRBV5-1, TRPS1, FAM104B, MIR4422HG 
##     SUPT4H1, PIP4K2A, CLDND1, PDZRN3, IMPDH2, ZSCAN5A, RAP1GDS1, ZNF211, TMEM131L, LINC00886 
## Negative:  SETBP1, NUP155, FANCA, CCL5, CLSPN, FANCB, ATAD5, CENPP, EXO1, E2F7 
##     IL12RB2, RHBDF2, SLC12A8, SLC12A2, HLA-DQA1, SFMBT2, BRIP1, RPL10A, BCL7A, LYAR 
## PC_ 5 
## Positive:  TSHZ2, RPS6KA2, CIB1, ABLIM1, AL136456.1, AC009522.1, SDCBP2-AS1, FUT7, RORA, DIPK2A 
##     TRBV5-1, TCTN1, APH1A, MAP7, PDIA4, EIF2S1, ARNTL2, SYCP2, MGAT5, NME1 
## Negative:  SESTD1, LYST, PECAM1, ALCAM, DTHD1, PTPN3, AL031599.1, RAP1GDS1, GZMK, IKZF2 
##     GALNT1, UBE2E2, CBLB, MCTP1, SFMBT2, STK33, ADGRA3, LINC02631, RNF14, AC093865.1 
##    Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
## 1      1   0.1740  3.000          0.792 147.000  148.0000 165.00
## 2      2   0.0256  0.487          0.748  80.800   80.6000 103.00
## 3      3   0.0485 -0.398          0.618  45.800   44.7000  66.50
## 4      4   0.2640 -0.732          0.550  27.000   25.4000  44.50
## 5      5   0.5050 -0.968          0.710  16.500   14.8000  31.70
## 6      6   0.6420 -1.090          0.738  10.500    8.8700  23.40
## 7      7   0.7070 -1.180          0.728   6.890    5.4600  17.80
## 8      8   0.7750 -1.260          0.789   4.710    3.4400  14.00
## 9      9   0.8010 -1.260          0.818   3.330    2.1600  11.20
## 10    10   0.8120 -1.230          0.813   2.420    1.4300   9.17
## 11    12   0.8640 -1.170          0.883   1.380    0.6830   6.34
## 12    14   0.7620 -1.200          0.764   0.854    0.3420   4.54
## 13    16   0.7800 -1.140          0.776   0.557    0.1740   3.32
## 14    18   0.8570 -1.080          0.882   0.379    0.0919   2.47
## 15    20   0.8420 -1.060          0.859   0.267    0.0499   1.86

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4   5   6   7   8   9 
## 144  24  23  19  14  13  10  10  10  10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 10 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
## $black
##  [1] "TUBA1B"    "SLC25A5"   "TYMS"      "TUBB"      "STMN1"     "TPI1"     
##  [7] "PSMA7"     "HIST1H4C"  "TK1"       "LDHA"      "HMGB2"     "TUBB4B"   
## [13] "BIRC5"     "CLSPN"     "HNRNPAB"   "MT2A"      "ENO1"      "KIF18B"   
## [19] "SPC25"     "MELK"      "CIT"       "ANLN"      "POLQ"      "RAD54L"   
## [25] "BRCA2"     "NCAPG2"    "PLK4"      "NUSAP1"    "MASTL"     "KNTC1"    
## [31] "BRIP1"     "ASPM"      "BUB1B"     "KIF14"     "CDCA8"     "KIF4A"    
## [37] "CKAP2L"    "ESPL1"     "HIST2H2AB" "CKS1B"     "ARHGAP11A" "NCAPH"    
## [43] "HJURP"     "KCNQ5"     "CDC45"     "SLBP"      "TIMM13"    "HSPD1"    
## [49] "DTL"       "MCM4"      "TRBV5-1"   "FANCA"     "FANCB"     "ATAD5"    
## [55] "CENPP"     "EXO1"      "E2F7"      "SLC12A8"   "BRCA1"     "MSH6"     
## [61] "FUT7"      "CX3CR1"    "UHRF1"     "WARS2"     "LRRC20"    "ACTL6A"   
## [67] "PIGM"     
## 
## $green
##  [1] "GAPDH"      "PFN1"       "ACTB"       "RPSA"       "HNRNPA1"   
##  [6] "ACTG1"      "CFL1"       "RPL28"      "B2M"        "RPL27A"    
## [11] "RPL11"      "RPL10"      "RPS19"      "RPS28"      "RPS12"     
## [16] "RPL30"      "RPL41"      "RPS23"      "RPS16"      "RPS29"     
## [21] "RPL13"      "RPS15A"     "RPL37A"     "RPLP1"      "RPS27"     
## [26] "RPS15"      "RPS18"      "RPL12"      "RPL18A"     "RPLP2"     
## [31] "RPS20"      "RPL18"      "LTB"        "RPS3A"      "TMSB10"    
## [36] "RPL10A"     "AC008937.2"
## 
## $red
##  [1] "PECAM1"     "MIR4422HG"  "RAP1GDS1"   "SESTD1"     "LYST"      
##  [6] "PTPN3"      "AL031599.1" "UBE2E2"     "STK33"      "DGKH"      
## 
## $brown
##  [1] "RHBDF2"     "BCL7A"      "AC009522.1" "APH1A"      "PDIA4"     
##  [6] "NME1"       "CDK2AP2"    "COBLL1"     "PIK3AP1"    "ATP1B1"    
## [11] "MZB1"       "METTL22"    "SYK"        "MRPL51"     "TRIO"      
## [16] "FGD4"       "NHP2"       "NOLC1"      "SLC8A1"    
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $black
##  [1] "TUBA1B"    "SLC25A5"   "TYMS"      "TUBB"      "STMN1"     "TPI1"     
##  [7] "PSMA7"     "HIST1H4C"  "TK1"       "LDHA"      "HMGB2"     "TUBB4B"   
## [13] "BIRC5"     "CLSPN"     "HNRNPAB"   "MT2A"      "ENO1"      "KIF18B"   
## [19] "SPC25"     "MELK"      "CIT"       "ANLN"      "POLQ"      "RAD54L"   
## [25] "BRCA2"     "NCAPG2"    "PLK4"      "NUSAP1"    "MASTL"     "KNTC1"    
## [31] "BRIP1"     "ASPM"      "BUB1B"     "KIF14"     "CDCA8"     "KIF4A"    
## [37] "CKAP2L"    "ESPL1"     "HIST2H2AB" "CKS1B"     "ARHGAP11A" "NCAPH"    
## [43] "HJURP"     "KCNQ5"     "CDC45"     "SLBP"      "TIMM13"    "HSPD1"    
## [49] "DTL"       "MCM4"      "TRBV5-1"   "FANCA"     "FANCB"     "ATAD5"    
## [55] "CENPP"     "EXO1"      "E2F7"      "SLC12A8"   "BRCA1"     "MSH6"     
## [61] "FUT7"      "CX3CR1"    "UHRF1"     "WARS2"     "LRRC20"    "ACTL6A"   
## [67] "PIGM"     
## 
## $green
##  [1] "GAPDH"      "PFN1"       "ACTB"       "RPSA"       "HNRNPA1"   
##  [6] "ACTG1"      "CFL1"       "RPL28"      "B2M"        "RPL27A"    
## [11] "RPL11"      "RPL10"      "RPS19"      "RPS28"      "RPS12"     
## [16] "RPL30"      "RPL41"      "RPS23"      "RPS16"      "RPS29"     
## [21] "RPL13"      "RPS15A"     "RPL37A"     "RPLP1"      "RPS27"     
## [26] "RPS15"      "RPS18"      "RPL12"      "RPL18A"     "RPLP2"     
## [31] "RPS20"      "RPL18"      "LTB"        "RPS3A"      "TMSB10"    
## [36] "RPL10A"     "AC008937.2"
## 
## $red
##  [1] "PECAM1"     "MIR4422HG"  "RAP1GDS1"   "SESTD1"     "LYST"      
##  [6] "PTPN3"      "AL031599.1" "UBE2E2"     "STK33"      "DGKH"      
## 
## $brown
##  [1] "RHBDF2"     "BCL7A"      "AC009522.1" "APH1A"      "PDIA4"     
##  [6] "NME1"       "CDK2AP2"    "COBLL1"     "PIK3AP1"    "ATP1B1"    
## [11] "MZB1"       "METTL22"    "SYK"        "MRPL51"     "TRIO"      
## [16] "FGD4"       "NHP2"       "NOLC1"      "SLC8A1"    
## 
## [1] "Naltrexone_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -1.9386
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.3206
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 2.2557e-30
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## Warning in irlba(A = t(x = object), nv = npcs, ...): You're computing too large
## a percentage of total singular values, use a standard svd instead.

## PC_ 1 
## Positive:  RRM2, POLQ, NCAPG2, KIF11, ECT2, DIAPH3, ASPM, KIF14, NCAPG, CDCA2 
##     DLGAP5, HIST1H3B, HIST1H1B, SPC25, TPX2, TOP2A, BRCA2, KIF15, CCDC150, NUF2 
## Negative:  PITPNC1, SESN3, AFF3, ZNF331, SLC2A3, MPP7, TSHZ2, AC137810.1, KIAA0825, MTRNR2L8 
##     TMEM164, PDE7A, AC104123.1, KCNQ1OT1, RAP2C-AS1, ATP11C, JUN, SNHG14, GRIK1, CD5 
## PC_ 2 
## Positive:  MTRNR2L8, CIT, HJURP, KIF11, TPX2, NCAPH, HIST1H4H, RRM2, KIF4A, HIST1H2AG 
##     DLGAP5, INCENP, HMGB2, GTSE1, POLQ, ASPM, PTMA, KIF15, HIST1H1B, KNL1 
## Negative:  ACO1, RFX3, CELF2, MUC20, KLF12, EXOC4, ZBTB20, N4BP1, TSHZ2, MBNL1 
##     AC106791.1, AL606491.1, TMEM63A, ANKMY1, ATXN1, MAP3K4, MGLL, LONRF1, RORA, AL050309.1 
## PC_ 3 
## Positive:  RPS23, RPS2, RPL41, RPS12, IL32, RPS16, TMSB10, FAU, RPS15, GAPDH 
##     ACTG1, B2M, RPL15, CRIP1, RPL21, RPS13, AC079793.1, PFN1, S100A4, MZT2B 
## Negative:  WWOX, E2F2, DDX11, ZNF367, RASA3, CD99L2, SPC25, KIFC1, LINC00265, CDK19 
##     AL136456.1, RAD51, POGLUT3, ATAD5, FOXP1, TACC3, CRACR2A, RNF144B, DEPDC1B, OTULINL 
## PC_ 4 
## Positive:  CCDC58, LINC00299, PROK2, DIP2C, KHDC1, ATPAF1, TPRG1L, TXNDC16, FILNC1, AC008549.2 
##     FARSB, FAM111B, RAI1, MCM4, ZNF71, PAK1, SDHAF3, CPEB3, PLD1, AC074032.1 
## Negative:  AL606491.1, AC079142.1, LIMK1, ZBTB24, HSF5, FIRRE, UBA6-AS1, PACS1, TSPAN17, CDRT4 
##     HCG17, TXK, DPH5, MRPS6, SLX4IP, ARHGAP11B, PRH1, AC092683.1, ENOX2, CENPV 
## PC_ 5 
## Positive:  SLC39A8, AC017071.1, G2E3-AS1, FILNC1, ZNF71, TNFAIP3, ELOVL4, PARL, EPHB1, LIPE-AS1 
##     ETV6, TIGAR, CRLS1, COPA, MYLIP, AP002807.1, ZNF331, PROSER3, CNOT6L, SMYD3 
## Negative:  COLQ, PPM1L, CENPP, HSF5, NKG7, AC017028.1, FSD1L, CCDC171, TBRG4, MRPL20-AS1 
##     GUSB, CDT1, NEXN, RUNX2, INSL6, PDCD11, ERLIN1, NUDCD1, ADCY3, UBE2A 
##    Power SFT.R.sq   slope truncated.R.sq mean.k. median.k. max.k.
## 1      1  0.37300 12.0000          0.819 165.000  165.0000 179.00
## 2      2  0.17800  2.7500          0.789  89.800   89.6000 107.00
## 3      3  0.00046 -0.0789          0.670  50.300   49.7000  69.10
## 4      4  0.17200 -1.1500          0.737  29.200   28.3000  47.80
## 5      5  0.42300 -1.5800          0.728  17.500   16.4000  35.30
## 6      6  0.58700 -1.5900          0.783  11.000    9.8000  27.40
## 7      7  0.74000 -1.6400          0.802   7.150    6.0500  22.30
## 8      8  0.79400 -1.9000          0.806   4.860    3.8400  18.60
## 9      9  0.86600 -1.8400          0.854   3.440    2.5400  15.90
## 10    10  0.90000 -1.7500          0.888   2.530    1.7000  13.90
## 11    12  0.91900 -1.6100          0.901   1.500    0.7830  10.90
## 12    14  0.96100 -1.4700          0.953   0.977    0.3980   8.76
## 13    16  0.94000 -1.4500          0.931   0.682    0.2210   7.20
## 14    18  0.94400 -1.4200          0.933   0.500    0.1270   6.01
## 15    20  0.95500 -1.3900          0.955   0.380    0.0733   5.07

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4   5   6   7   8   9  10  11  12 
## 119  25  25  20  18  18  16  16  12  12  11  10  10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 13 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 9 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 9 module eigengenes in given set.
## $magenta
##  [1] "RRM2"      "POLQ"      "NCAPG2"    "KIF11"     "ECT2"      "DIAPH3"   
##  [7] "ASPM"      "KIF14"     "NCAPG"     "CDCA2"     "DLGAP5"    "HIST1H3B" 
## [13] "HIST1H1B"  "SPC25"     "TPX2"      "TOP2A"     "BRCA2"     "KIF15"    
## [19] "CCDC150"   "NUF2"      "CDCA8"     "FANCI"     "STMN1"     "TMPO"     
## [25] "MKI67"     "CIT"       "HJURP"     "NCAPH"     "HIST1H4H"  "KIF4A"    
## [31] "HIST1H2AG" "INCENP"    "HMGB2"     "GTSE1"     "KNL1"      "AURKB"    
## [37] "HIST1H2AH" "ANLN"      "E2F2"      "DDX11"     "ZNF367"    "CD99L2"   
## [43] "KIFC1"     "LINC00265" "CDK19"     "RAD51"     "ATAD5"     "TACC3"    
## [49] "RNF144B"   "DEPDC1B"   "E2F8"      "MPC1"      "WDR76"     "MCM4"     
## [55] "CENPP"     "MED26"     "INPP5F"   
## 
## $greenyellow
##  [1] "MPP7"     "SNX8"     "ASPH"     "ALAD"     "MAN2B2"   "TTC23L"  
##  [7] "BLK"      "CLECL1"   "EFL1"     "SGO1-AS1"
## 
## $turquoise
##  [1] "PTMA"       "RPS23"      "RPS2"       "RPL41"      "RPS12"     
##  [6] "IL32"       "RPS16"      "TMSB10"     "FAU"        "RPS15"     
## [11] "GAPDH"      "ACTG1"      "B2M"        "RPL15"      "CRIP1"     
## [16] "RPL21"      "RPS13"      "AC079793.1" "PFN1"       "S100A4"    
## [21] "MZT2B"      "VIM"        "ACTB"       "RPS11"      "RPL38"     
## 
## $green
##  [1] "ACO1"        "AL606491.1"  "TMEM63A"     "DPH5"        "AC079142.1" 
##  [6] "LIMK1"       "ZBTB24"      "HSF5"        "FIRRE"       "UBA6-AS1"   
## [11] "TSPAN17"     "CDRT4"       "HCG17"       "MRPS6"       "SLX4IP"     
## [16] "PRH1"        "ENOX2"       "CENPV"       "ARHGEF3"     "LRRC8D"     
## [21] "COLQ"        "ATG4C"       "ALG14"       "HAPLN3"      "KCNMB4"     
## [26] "C8orf37-AS1" "PPME1"       "TMEM106B"    "ZC3HC1"      "SLC7A1"     
## 
## $black
##  [1] "CCDC58"     "PROK2"      "FILNC1"     "AC008549.2" "ZNF71"     
##  [6] "PAK1"       "SDHAF3"     "TTN-AS1"    "FRY"        "CCP110"    
## [11] "AC017071.1" "ELOVL4"     "PARL"       "EPHB1"      "LIPE-AS1"  
## [16] "CRLS1"      "AP002807.1" "PROSER3"    "APAF1"      "PGRMC2"    
## [21] "AL365255.1" "ZKSCAN8"    "PTPDC1"     "B3GNT5"     "C5orf17"   
## [26] "PARD6B"    
## 
## $red
##  [1] "TXNDC16"    "RAI1"       "NKG7"       "AC017028.1" "TBRG4"     
##  [6] "MRPL20-AS1" "GUSB"       "CDT1"       "INSL6"      "ERLIN1"    
## [11] "UBE2A"      "IFI44L"     "AC004551.1" "POFUT1"     "ASPN"      
## [16] "L2HGDH"    
## 
## $purple
##  [1] "AC092683.1" "TRIO"       "ZNF549"     "DYNC2LI1"   "ANKMY2"    
##  [6] "UBE3C"      "AL360270.1" "CD302"      "NCDN"       "MTHFS"     
## [11] "NAB1"      
## 
## $yellow
##  [1] "PPM1L"      "FSD1L"      "PDCD11"     "ADCY3"      "PHLPP2"    
##  [6] "AC068631.1" "WDR27"      "CERS4"      "CDK14"      "ZBTB2"     
## [11] "CHCHD6"     "LINC00899"  "EFCAB2"     "ST7"        "FBXL3"     
## [16] "TSEN15"     "DNM3"       "INTU"      
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "10/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "1/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $magenta
##  [1] "RRM2"      "POLQ"      "NCAPG2"    "KIF11"     "ECT2"      "DIAPH3"   
##  [7] "ASPM"      "KIF14"     "NCAPG"     "CDCA2"     "DLGAP5"    "HIST1H3B" 
## [13] "HIST1H1B"  "SPC25"     "TPX2"      "TOP2A"     "BRCA2"     "KIF15"    
## [19] "CCDC150"   "NUF2"      "CDCA8"     "FANCI"     "STMN1"     "TMPO"     
## [25] "MKI67"     "CIT"       "HJURP"     "NCAPH"     "HIST1H4H"  "KIF4A"    
## [31] "HIST1H2AG" "INCENP"    "HMGB2"     "GTSE1"     "KNL1"      "AURKB"    
## [37] "HIST1H2AH" "ANLN"      "E2F2"      "DDX11"     "ZNF367"    "CD99L2"   
## [43] "KIFC1"     "LINC00265" "CDK19"     "RAD51"     "ATAD5"     "TACC3"    
## [49] "RNF144B"   "DEPDC1B"   "E2F8"      "MPC1"      "WDR76"     "MCM4"     
## [55] "CENPP"     "MED26"     "INPP5F"   
## 
## $greenyellow
##  [1] "MPP7"     "SNX8"     "ASPH"     "ALAD"     "MAN2B2"   "TTC23L"  
##  [7] "BLK"      "CLECL1"   "EFL1"     "SGO1-AS1"
## 
## $turquoise
##  [1] "PTMA"       "RPS23"      "RPS2"       "RPL41"      "RPS12"     
##  [6] "IL32"       "RPS16"      "TMSB10"     "FAU"        "RPS15"     
## [11] "GAPDH"      "ACTG1"      "B2M"        "RPL15"      "CRIP1"     
## [16] "RPL21"      "RPS13"      "AC079793.1" "PFN1"       "S100A4"    
## [21] "MZT2B"      "VIM"        "ACTB"       "RPS11"      "RPL38"     
## 
## $green
##  [1] "ACO1"        "AL606491.1"  "TMEM63A"     "DPH5"        "AC079142.1" 
##  [6] "LIMK1"       "ZBTB24"      "HSF5"        "FIRRE"       "UBA6-AS1"   
## [11] "TSPAN17"     "CDRT4"       "HCG17"       "MRPS6"       "SLX4IP"     
## [16] "PRH1"        "ENOX2"       "CENPV"       "ARHGEF3"     "LRRC8D"     
## [21] "COLQ"        "ATG4C"       "ALG14"       "HAPLN3"      "KCNMB4"     
## [26] "C8orf37-AS1" "PPME1"       "TMEM106B"    "ZC3HC1"      "SLC7A1"     
## 
## $black
##  [1] "CCDC58"     "PROK2"      "FILNC1"     "AC008549.2" "ZNF71"     
##  [6] "PAK1"       "SDHAF3"     "TTN-AS1"    "FRY"        "CCP110"    
## [11] "AC017071.1" "ELOVL4"     "PARL"       "EPHB1"      "LIPE-AS1"  
## [16] "CRLS1"      "AP002807.1" "PROSER3"    "APAF1"      "PGRMC2"    
## [21] "AL365255.1" "ZKSCAN8"    "PTPDC1"     "B3GNT5"     "C5orf17"   
## [26] "PARD6B"    
## 
## $red
##  [1] "TXNDC16"    "RAI1"       "NKG7"       "AC017028.1" "TBRG4"     
##  [6] "MRPL20-AS1" "GUSB"       "CDT1"       "INSL6"      "ERLIN1"    
## [11] "UBE2A"      "IFI44L"     "AC004551.1" "POFUT1"     "ASPN"      
## [16] "L2HGDH"    
## 
## $purple
##  [1] "AC092683.1" "TRIO"       "ZNF549"     "DYNC2LI1"   "ANKMY2"    
##  [6] "UBE3C"      "AL360270.1" "CD302"      "NCDN"       "MTHFS"     
## [11] "NAB1"      
## 
## $yellow
##  [1] "PPM1L"      "FSD1L"      "PDCD11"     "ADCY3"      "PHLPP2"    
##  [6] "AC068631.1" "WDR27"      "CERS4"      "CDK14"      "ZBTB2"     
## [11] "CHCHD6"     "LINC00899"  "EFCAB2"     "ST7"        "FBXL3"     
## [16] "TSEN15"     "DNM3"       "INTU"      
## 
## [1] "Naltrexone_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -1.7594
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.32006
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 6.3047e-30
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## Warning in irlba(A = t(x = object), nv = npcs, ...): You're computing too large
## a percentage of total singular values, use a standard svd instead.

## PC_ 1 
## Positive:  BTBD9, GFPT1, FLI1, SLC16A7, CAPZA2, CMC2, AL136456.1, RAB3GAP1, AC008124.1, ZMYM2 
##     ZDHHC2, DCUN1D2, TTC13, AC005237.1, ATP13A3, ABLIM1, CNOT4, PPP2R5C, KIAA1109, SKAP1 
## Negative:  MTRNR2L8, RPL28, RPLP1, TMSB10, RPS23, RPL12, PTMA, RPL37A, RPL19, HIST1H4C 
##     TMSB4X, PFN1, RPS20, RPS15, RPS19, PCNA, RPL10, EEF1A1, EIF2B2, AC243829.2 
## PC_ 2 
## Positive:  MALAT1, EPHA4, TSHZ2, ANK3, LDLRAD4, PVT1, SNX29, PRKCA, NOL4L, MGAT4A 
##     ZC3H12D, TTC39C, TRAF3IP2-AS1, ZMIZ1, ATP10A, AL138720.1, TAFA1, EEF2K, LINC02649, PIGZ 
## Negative:  ACTB, SH3BGRL3, TMSB10, EEF1A1, UBE2A, RPS15, RPS2, RPLP1, RPL41, RPL8 
##     CD52, RPS3, RPL36A, S100A4, TMSB4X, RPL28, RORA-AS1, RPS19, RPL37A, RPL37 
## PC_ 3 
## Positive:  IL26, VWDE, ATP6V0A1, ERN1, CEP57, DMAC2L, P4HA1, CRADD, TMPRSS3, RORA 
##     PTPN13, SMIM12, FDX1, UBE2E3, IL18RAP, DEPDC5, FASTKD3, TC2N, EHBP1, IL12RB2 
## Negative:  PCAT1, PGM2L1, PTPN3, AC027018.1, SESTD1, AFF3, SESN3, NCOA1, UPP1, TIGIT 
##     CDRT4, CNR2, MIR4422HG, GFOD1, LYST, AC023906.5, STAU2, GPD2, GNAQ, AL157911.1 
## PC_ 4 
## Positive:  BRIP1, AP001831.1, POLE, NLGN4Y, TRERF1, AC006206.2, GCNT2, NCAPG, FANCA, POLE2 
##     VAMP3, PLEKHG1, ITGB3BP, SPC25, WDR62, KNL1, SETD4, MTURN, COPG2, CEP295 
## Negative:  SMCO4, AC016831.1, AC009315.1, PKIA-AS1, ICA1, AC090825.1, AL592429.2, AC023790.2, CAMK2D, PIGU 
##     IL2RA, POU5F2, AL589693.1, AC005703.4, FRMD4A, BMT2, PITPNM2, TXK, AC131237.1, SAMD4A 
## PC_ 5 
## Positive:  DTL, ZNF587B, GMNN, SKA2, SPC25, WDR62, CIT, ZNF367, ATAD5, PKD2 
##     AC093865.1, CATSPERE, CTSA, ST3GAL4, CSRNP2, SESTD1, FANCA, MAP3K20, KNL1, HIST1H4H 
## Negative:  ANK3, FAU, INPP4B, LIME1, CD226, TSHZ2, RPS23, PI4K2A, RABAC1, MIAT 
##     GCNT4, FAM24B, MAP3K1, PAG1, IL7R, LTB, AC079921.1, PCED1B, ST8SIA1, TMBIM4 
##    Power SFT.R.sq   slope truncated.R.sq mean.k. median.k. max.k.
## 1      1  0.34200 41.1000          0.188 208.000  208.0000 225.00
## 2      2  0.31500 19.2000          0.146 113.000  113.0000 133.00
## 3      3  0.47500  4.6800          0.651  63.300   63.1000  81.30
## 4      4  0.36100  2.6300          0.775  36.500   36.1000  51.50
## 5      5  0.26000  1.6900          0.815  21.700   21.4000  33.80
## 6      6  0.09760  0.8250          0.894  13.300   13.0000  23.00
## 7      7  0.00039  0.0425          0.860   8.480    8.2100  16.40
## 8      8  0.02070 -0.2500          0.831   5.560    5.3300  12.10
## 9      9  0.14700 -0.6190          0.800   3.770    3.4800   9.44
## 10    10  0.43500 -1.1500          0.828   2.630    2.3400   8.09
## 11    12  0.76700 -1.8700          0.801   1.400    1.1000   6.34
## 12    14  0.85700 -1.9600          0.842   0.830    0.5550   5.26
## 13    16  0.92200 -1.8500          0.921   0.539    0.2950   4.52
## 14    18  0.92800 -1.7300          0.914   0.378    0.1660   3.99
## 15    20  0.91800 -1.6200          0.895   0.282    0.0972   3.59

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4 
## 353  11  10  10  10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 4 module eigengenes in given set.
## $yellow
##  [1] "DMAC2L"    "SMIM12"    "IL12RB2"   "C4orf48"   "IFI44L"    "CCDC112"  
##  [7] "PSAT1"     "KEAP1"     "CLIP1-AS1" "NIT2"     
## 
## $brown
##  [1] "BRIP1"      "POLE"       "FANCA"      "POLE2"      "SPC25"     
##  [6] "WDR62"      "KNL1"       "COPG2"      "GMNN"       "CBX1"      
## [11] "AC008770.3" "CIT"        "ZNF367"     "ATAD5"      "MAP3K20"   
## [16] "KNTC1"      "DPH5"       "AHDC1"      "ZNF461"     "KIAA1841"  
## [21] "NAV1"      
## 
## $blue
##  [1] "AC016831.1" "AC009315.1" "AL592429.2" "POU5F2"     "AC093010.2"
##  [6] "LINC02656"  "TTYH2"      "CLVS1"      "FRG1-DT"    "SFXN2"     
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $yellow
##  [1] "DMAC2L"    "SMIM12"    "IL12RB2"   "C4orf48"   "IFI44L"    "CCDC112"  
##  [7] "PSAT1"     "KEAP1"     "CLIP1-AS1" "NIT2"     
## 
## $brown
##  [1] "BRIP1"      "POLE"       "FANCA"      "POLE2"      "SPC25"     
##  [6] "WDR62"      "KNL1"       "COPG2"      "GMNN"       "CBX1"      
## [11] "AC008770.3" "CIT"        "ZNF367"     "ATAD5"      "MAP3K20"   
## [16] "KNTC1"      "DPH5"       "AHDC1"      "ZNF461"     "KIAA1841"  
## [21] "NAV1"      
## 
## $blue
##  [1] "AC016831.1" "AC009315.1" "AL592429.2" "POU5F2"     "AC093010.2"
##  [6] "LINC02656"  "TTYH2"      "CLVS1"      "FRG1-DT"    "SFXN2"     
## 
## [1] "Methadone_3"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -1.6521
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.31961
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 0
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## Error in irlba(A = t(x = object), nv = npcs, ...) : 
##   max(nu, nv) must be strictly less than min(nrow(A), ncol(A))
## [1] "Methadone_0"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : at -1.1302
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : radius 0.00026289
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : all data on boundary of neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -1.1302
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.016214
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : zero-width neighborhood. make span bigger

## Error in irlba(A = t(x = object), nv = npcs, ...) : 
##   max(nu, nv) must be strictly less than min(nrow(A), ncol(A))
saveRDS(mods1, "~/gibbs/DOGMAMORPH/Ranalysis/modules/20230529ProliferatingModules_Treatment_Timepoint.rds")

#just doing treatment, we get at least 2 per condition 
results.split<-SplitObject(results, "Treatment")
conds<-cbind(c(8, 7,6),c(6, 9,8))
mods2<-WrapGroupModID(results.split, "NA", conds)
## [1] "Bup.Nalo"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.541
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.49964
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 6.0552e-16
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1 
## Positive:  ANK3, PCAT1, FAAH2, TTN, ABLIM1, DDX60L, MAML2, AL136456.1, PITPNC1, SESN3 
##     NEAT1, ZHX2, SORL1, PPP1R16B, XIST, FMN1, CMTM8, LEF1, UST, DLGAP1 
## Negative:  TUBA1B, TUBB, STMN1, HIST1H4C, RRM2, GAPDH, DIAPH3, TYMS, HMGB2, TK1 
##     HIST1H3B, PCLAF, FBXO5, HIST1H1B, TMPO, POLQ, NCAPG, NUSAP1, PFN1, PCNA 
## PC_ 2 
## Positive:  RPL28, RPL41, RPL18A, RPL13A, RPL27A, RPS28, RPS19, RPS15, RPL11, RPS18 
##     RPS12, B2M, RPS27, RPL18, RPS23, RPS29, RPS2, RPS16, RPL37, RPLP1 
## Negative:  POLQ, NCAPG, CIT, KIF18B, DIAPH3, KIF15, ATAD5, SPC25, NCAPG2, BRCA2 
##     RRM2, KNTC1, BRIP1, DTL, NUSAP1, ASPM, KNL1, MKI67, CDCA2, TOP2A 
## PC_ 3 
## Positive:  KIF14, KIF4A, PLK1, AURKA, LTB, UBE2C, NEAT1, HMMR, KIF20A, TSHZ2 
##     CCNF, SESN3, KIF23, CDCA2, CKAP2L, CDCA8, ASPM, SGO2, ESPL1, KIF18B 
## Negative:  PECAM1, MIR4422HG, PTPN3, LYST, NKG7, GZMK, AGAP1, KLRK1, MCTP2, DTHD1 
##     KCNQ5, AL031599.1, NCOA1, CNR2, UBE2E2, GZMA, SFMBT2, SESTD1, SLBP, AFF3 
## PC_ 4 
## Positive:  MIR4422HG, PTPN3, DTHD1, PECAM1, UBE2E2, AL031599.1, LYST, SESTD1, GZMK, PACSIN1 
##     AFF3, PGM2L1, ANTXR2, RUNX2, LZTFL1, CBLB, CD38, CCNG2, BACH2, CENPA 
## Negative:  MSH6, FANCA, UHRF1, CLSPN, TRERF1, GPHN, EXO1, DTL, MPP6, NDUFAF6 
##     CDC45, MCOLN2, MCM4, PUS7, CCNE2, MCM10, ORC6, E2F7, HELLS, FKBP5 
## PC_ 5 
## Positive:  PLCL1, STAM, TXK, CDHR3, AL136456.1, MGAT5, MAST4, ABLIM1, WDFY2, MCF2L2 
##     SNX29, SMYD3, ELP4, MGAT4A, ZC2HC1A, AL121935.1, ZNRF1, LINC01876, SNX9, CASK 
## Negative:  CCL5, NKG7, TGFBR3, TOP2A, CENPF, CDCA2, GZMH, HIST1H2BH, CD8B, GTSE1 
##     GZMA, KIF2C, AOAH, HIST1H3B, C1orf21, CCNB2, KIF14, PLK1, HIST2H2AA4, KLRD1 
##    Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
## 1      1  0.00387 -0.524         0.3390 161.000  159.0000 179.00
## 2      2  0.20800 -1.900         0.4850  86.300   83.5000 110.00
## 3      3  0.60800 -2.430         0.7210  47.400   44.2000  70.60
## 4      4  0.68700 -2.150         0.7140  26.800   23.7000  47.80
## 5      5  0.77100 -2.060         0.7450  15.700   12.8000  33.80
## 6      6  0.82800 -1.900         0.7950   9.500    7.0800  24.80
## 7      7  0.79600 -1.680         0.7490   5.970    3.9000  18.70
## 8      8  0.82900 -1.540         0.7970   3.900    2.1900  14.50
## 9      9  0.78400 -1.460         0.7460   2.650    1.2300  11.40
## 10    10  0.70400 -1.390         0.6400   1.850    0.7070   9.13
## 11    12  0.20700 -2.560         0.1010   0.991    0.2440   6.05
## 12    14  0.20500 -2.230         0.1140   0.576    0.0916   4.17
## 13    16  0.21300 -2.110         0.1440   0.355    0.0353   2.94
## 14    18  0.79800 -1.110         0.7900   0.227    0.0159   2.11
## 15    20  0.19400 -1.890         0.0187   0.149    0.0066   1.54

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##  0  1  2  3  4  5  6  7  8  9 10 11 
## 84 38 29 27 25 20 19 18 16 11 11 10

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 12 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 8 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 8 module eigengenes in given set.
## $turquoise
##  [1] "ANK3"    "MAML2"   "SORL1"   "XIST"    "FMN1"    "GAPDH"   "PFN1"   
##  [8] "ACTB"    "RPL28"   "RPL41"   "RPL18A"  "RPL13A"  "RPL27A"  "RPS28"  
## [15] "RPS19"   "RPS15"   "RPL11"   "RPS18"   "RPS12"   "B2M"     "RPS27"  
## [22] "RPL18"   "RPS23"   "RPS29"   "RPS2"    "RPS16"   "RPL37"   "RPLP1"  
## [29] "RPL30"   "RPL10"   "RPS11"   "RPS27A"  "RPLP2"   "LTB"     "SNED1"  
## [36] "ATP5F1E" "PLAC8"   "RPS24"  
## 
## $greenyellow
##  [1] "TTN"        "SESN3"      "LEF1"       "PGM2L1"     "AP000787.1"
##  [6] "AC093865.1" "IKZF2"      "FHIT"       "RBMS3"      "MAGI1"     
## 
## $pink
##  [1] "ABLIM1"     "AL136456.1" "NEAT1"      "HMGN2"      "H2AFZ"     
##  [6] "TSHZ2"      "APOLD1"     "ANTXR2"     "RUNX2"      "BACH2"     
## [11] "PLCL1"      "STAM"       "CDHR3"      "MGAT5"      "MAST4"     
## [16] "WDFY2"      "SNX29"      "SMYD3"      "ELP4"       "MGAT4A"    
## [21] "AL121935.1" "SNX9"       "CASK"       "RFX3-AS1"   "SAMD12"    
## [26] "ARHGAP10"   "ADK"        "TROAP"      "RORA"       "PRKY"      
## [31] "UTY"        "IL2RA"      "AL589693.1" "COL5A3"     "USP9Y"     
## [36] "CLIC5"      "ANP32E"     "NCALD"      "CAMK2D"     "LGMN"      
## [41] "SGO1-AS1"  
## 
## $green
##  [1] "TUBA1B"     "TUBB"       "STMN1"      "HIST1H4C"   "RRM2"      
##  [6] "DIAPH3"     "HMGB2"      "HIST1H3B"   "FBXO5"      "HIST1H1B"  
## [11] "TMPO"       "POLQ"       "NCAPG"      "NUSAP1"     "MKI67"     
## [16] "SMC2"       "CIT"        "KIF18B"     "KIF15"      "ATAD5"     
## [21] "SPC25"      "NCAPG2"     "BRCA2"      "KNTC1"      "BRIP1"     
## [26] "DTL"        "ASPM"       "KNL1"       "CDCA2"      "TOP2A"     
## [31] "BUB1B"      "ZGRF1"      "CIP2A"      "ANLN"       "FANCA"     
## [36] "KIF14"      "KIF4A"      "PLK1"       "AURKA"      "UBE2C"     
## [41] "HMMR"       "KIF20A"     "CCNF"       "KIF23"      "CKAP2L"    
## [46] "CDCA8"      "SGO2"       "ESPL1"      "CCNB1"      "INCENP"    
## [51] "HIST2H2AA4" "SLBP"       "CENPA"      "MSH6"       "UHRF1"     
## [56] "CLSPN"      "GPHN"       "EXO1"       "CDC45"      "MCOLN2"    
## [61] "MCM4"       "PUS7"       "CCNE2"      "MCM10"      "ORC6"      
## [66] "E2F7"       "HELLS"      "FAM111B"    "TBXAS1"     "ECM2"      
## [71] "CENPF"      "HIST1H2BH"  "GTSE1"      "KIF2C"      "CCNB2"     
## [76] "HIST1H3D"   "HIST1H3F"   "HIST1H2AI"  "SLC35A4"    "JARID2"    
## [81] "HSP90AA1"   "DAD1"       "CDC20"      "CALM1"      "ZWINT"     
## [86] "DMC1"       "CCDC34"     "HIST1H2BO"  "HMGA1"      "HIST1H2BK" 
## [91] "MAGI3"      "MSC-AS1"    "HIST1H3G"   "DEPDC1"     "PAICS"     
## 
## $magenta
##  [1] "PECAM1"     "MIR4422HG"  "PTPN3"      "LYST"       "GZMK"      
##  [6] "AGAP1"      "DTHD1"      "AL031599.1" "UBE2E2"     "GALNT1"    
## [11] "CBLB"      
## 
## $black
##  [1] "NKG7"       "KLRK1"      "GZMA"       "CD8B"       "MVB12B"    
##  [6] "TRERF1"     "CCL5"       "GZMH"       "AOAH"       "C1orf21"   
## [11] "KLRD1"      "ZEB2"       "CTSW"       "PPP2R2B"    "PDGFD"     
## [16] "MATK"       "TRGC2"      "AC022075.1"
## 
## $purple
##  [1] "AGPAT4" "GPR15"  "SCMH1"  "SYTL2"  "IGF1R"  "ZBTB16" "SELL"   "ROR2"  
##  [9] "DEC1"   "DOCK3"  "PDE8A" 
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "8389/10000 permutations failed the Mann-Whitney test."
## [1] "7760/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "1831/10000 permutations failed the Mann-Whitney test."
## [1] "5387/10000 permutations failed the Mann-Whitney test."
## [1] "9466/10000 permutations failed the Mann-Whitney test."
## $turquoise
##  [1] "ANK3"    "MAML2"   "SORL1"   "XIST"    "FMN1"    "GAPDH"   "PFN1"   
##  [8] "ACTB"    "RPL28"   "RPL41"   "RPL18A"  "RPL13A"  "RPL27A"  "RPS28"  
## [15] "RPS19"   "RPS15"   "RPL11"   "RPS18"   "RPS12"   "B2M"     "RPS27"  
## [22] "RPL18"   "RPS23"   "RPS29"   "RPS2"    "RPS16"   "RPL37"   "RPLP1"  
## [29] "RPL30"   "RPL10"   "RPS11"   "RPS27A"  "RPLP2"   "LTB"     "SNED1"  
## [36] "ATP5F1E" "PLAC8"   "RPS24"  
## 
## $green
##  [1] "TUBA1B"     "TUBB"       "STMN1"      "HIST1H4C"   "RRM2"      
##  [6] "DIAPH3"     "HMGB2"      "HIST1H3B"   "FBXO5"      "HIST1H1B"  
## [11] "TMPO"       "POLQ"       "NCAPG"      "NUSAP1"     "MKI67"     
## [16] "SMC2"       "CIT"        "KIF18B"     "KIF15"      "ATAD5"     
## [21] "SPC25"      "NCAPG2"     "BRCA2"      "KNTC1"      "BRIP1"     
## [26] "DTL"        "ASPM"       "KNL1"       "CDCA2"      "TOP2A"     
## [31] "BUB1B"      "ZGRF1"      "CIP2A"      "ANLN"       "FANCA"     
## [36] "KIF14"      "KIF4A"      "PLK1"       "AURKA"      "UBE2C"     
## [41] "HMMR"       "KIF20A"     "CCNF"       "KIF23"      "CKAP2L"    
## [46] "CDCA8"      "SGO2"       "ESPL1"      "CCNB1"      "INCENP"    
## [51] "HIST2H2AA4" "SLBP"       "CENPA"      "MSH6"       "UHRF1"     
## [56] "CLSPN"      "GPHN"       "EXO1"       "CDC45"      "MCOLN2"    
## [61] "MCM4"       "PUS7"       "CCNE2"      "MCM10"      "ORC6"      
## [66] "E2F7"       "HELLS"      "FAM111B"    "TBXAS1"     "ECM2"      
## [71] "CENPF"      "HIST1H2BH"  "GTSE1"      "KIF2C"      "CCNB2"     
## [76] "HIST1H3D"   "HIST1H3F"   "HIST1H2AI"  "SLC35A4"    "JARID2"    
## [81] "HSP90AA1"   "DAD1"       "CDC20"      "CALM1"      "ZWINT"     
## [86] "DMC1"       "CCDC34"     "HIST1H2BO"  "HMGA1"      "HIST1H2BK" 
## [91] "MAGI3"      "MSC-AS1"    "HIST1H3G"   "DEPDC1"     "PAICS"     
## 
## [1] "Naltrexone"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.1607
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.32185
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 2.7607e-31
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619

## PC_ 1 
## Positive:  NCAPG2, DIAPH3, NCAPG, KIF14, POLQ, RRM2, SPC25, ATAD5, TOP2A, CCDC150 
##     BRCA2, E2F8, BARD1, LMNB1, KIF11, HIST1H3B, RUNX1, CENPK, CDCA2, CDCA8 
## Negative:  MTRNR2L8, JUN, AFF3, AC243829.2, ZNF331, PGAM5, RBFOX3, JUNB, AC137810.1, RBMS3 
##     KCNQ1OT1, EFCAB8, AC105402.3, RILPL2, CCDC102B, RPS19, GRIK1, DEC1, RAP2C-AS1, LINC01505 
## PC_ 2 
## Positive:  KIF11, DIAPH3, RRM2, POLQ, ASPM, HIST1H3B, KIF14, CDCA8, NCAPG, FANCI 
##     STIL, SPC25, TPX2, HIST1H1B, HIST1H4H, DLGAP5, SHCBP1, CIT, INCENP, NUSAP1 
## Negative:  ZBTB20, ANK3, TSHZ2, KLF12, CD28, TC2N, RFX3, CELF2, PRKCA, SERINC5 
##     ABLIM1, ARID1B, RNASET2, EPHA4, GABPB1-AS1, CAMKMT, INPP4B, ACYP2, TSPOAP1-AS1, MAML2 
## PC_ 3 
## Positive:  DTHD1, SESTD1, CEP128, LDLRAD4, PTPN3, MIR4422HG, AFF3, E2F3, AGAP1, TRPS1 
##     FOXP1, TTN, TXK, BCL2, PCAT1, MYB, HAVCR2, PECAM1, SOS2, CNR2 
## Negative:  RPS2, CD52, IL32, RPL41, RPS19, RPS16, CRIP1, FAU, LTB, TMSB10 
##     RPS15, S100A4, ACTG1, GAPDH, RPS28, RPL23, ACTB, LINC02694, RPS13, ATP5PF 
## PC_ 4 
## Positive:  PTPN3, SESTD1, MCTP2, AFF3, UBE2E2, PCAT1, RPS15, LYST, MIR4422HG, PGM2L1 
##     CNR2, PECAM1, RPL41, RPS2, TIGIT, AC104078.2, ANTXR2, DTHD1, TMSB10, AC093019.2 
## Negative:  TTC39C, RORA, PTPN13, AL136456.1, FRY, FLI1, IL18R1, GRAMD1B, LINC00299, ERN1 
##     ADAM19, HIVEP3, MAP3K1, SAMD8, RPS6KA3, EGLN3, TC2N, TMPRSS3, PAG1, ETV6 
## PC_ 5 
## Positive:  MALAT1, INPP4B, JUNB, TSHZ2, IMMP2L, MPP7, ANK3, TNFAIP3, FOS, UST 
##     FOSB, RGCC, ST6GALNAC3, DISC1, AP000787.1, RNASET2, CCR7, SNED1, TUBB4B, HIST1H3F 
## Negative:  USP18, NKG7, GZMA, HLA-DQA2, AC017028.1, INSL6, RHEBL1, MRPL20-AS1, IL18RAP, GOLIM4 
##     AC004551.1, CDT1, ATG16L2, FECH, ARHGEF7, CCL5, TMPRSS3, IL26, HLA-DRB1, RPTOR 
##    Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1      1   0.5730 24.50        0.91000 154.000  154.0000 161.00
## 2      2   0.1560  4.89        0.70100  81.000   80.9000  91.40
## 3      3   0.0339 -1.12        0.76900  43.500   43.2000  55.10
## 4      4   0.2810 -2.33        0.56000  24.000   23.5000  35.60
## 5      5   0.4800 -2.60        0.50600  13.600   13.0000  24.50
## 6      6   0.5990 -2.29        0.53300   7.950    7.3500  17.90
## 7      7   0.6620 -2.10        0.56900   4.830    4.1400  13.80
## 8      8   0.7620 -2.06        0.69500   3.060    2.3900  11.00
## 9      9   0.8450 -1.96        0.81500   2.020    1.4300   9.00
## 10    10   0.8190 -1.80        0.79700   1.390    0.8690   7.57
## 11    12   0.9090 -1.54        0.89100   0.733    0.3350   5.56
## 12    14   0.8830 -1.40        0.85800   0.438    0.1400   4.19
## 13    16   0.8810 -1.30        0.85300   0.286    0.0627   3.21
## 14    18   0.8630 -1.25        0.82500   0.198    0.0298   2.48
## 15    20   0.2060 -2.00        0.00753   0.143    0.0143   1.94

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4   5 
## 213  26  19  14  14  12

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 6 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
## $green
##  [1] "NCAPG2"    "DIAPH3"    "NCAPG"     "KIF14"     "POLQ"      "RRM2"     
##  [7] "SPC25"     "ATAD5"     "TOP2A"     "CCDC150"   "BRCA2"     "E2F8"     
## [13] "BARD1"     "LMNB1"     "KIF11"     "HIST1H3B"  "CENPK"     "CDCA2"    
## [19] "CDCA8"     "FANCI"     "CCNF"      "ASPM"      "CIP2A"     "STIL"     
## [25] "TPX2"      "HIST1H1B"  "HIST1H4H"  "DLGAP5"    "SHCBP1"    "CIT"      
## [31] "INCENP"    "NUSAP1"    "HIST1H2AH" "KNL1"      "KIF4A"     "ANLN"     
## [37] "HIST1H3F"  "RFC3"     
## 
## $brown
##  [1] "AFF3"      "DTHD1"     "SESTD1"    "PTPN3"     "MIR4422HG" "MYB"      
##  [7] "HAVCR2"    "PECAM1"    "LINC02320" "HAVCR1"    "MCTP2"     "UBE2E2"   
## [13] "LYST"      "TIGIT"    
## 
## $blue
##  [1] "RPS19"  "RPS2"   "CD52"   "IL32"   "RPL41"  "RPS16"  "CRIP1"  "FAU"   
##  [9] "LTB"    "TMSB10" "RPS15"  "S100A4" "ACTG1"  "GAPDH"  "RPS28"  "RPL23" 
## [17] "ACTB"   "RPS13"  "S100A6"
## 
## $yellow
##  [1] "ATP5PF"     "USP18"      "HLA-DQA2"   "AC017028.1" "INSL6"     
##  [6] "RHEBL1"     "MRPL20-AS1" "GOLIM4"     "AC004551.1" "CDT1"      
## [11] "HLA-DRB1"   "IFI6"       "C2orf92"    "TRIM21"    
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $green
##  [1] "NCAPG2"    "DIAPH3"    "NCAPG"     "KIF14"     "POLQ"      "RRM2"     
##  [7] "SPC25"     "ATAD5"     "TOP2A"     "CCDC150"   "BRCA2"     "E2F8"     
## [13] "BARD1"     "LMNB1"     "KIF11"     "HIST1H3B"  "CENPK"     "CDCA2"    
## [19] "CDCA8"     "FANCI"     "CCNF"      "ASPM"      "CIP2A"     "STIL"     
## [25] "TPX2"      "HIST1H1B"  "HIST1H4H"  "DLGAP5"    "SHCBP1"    "CIT"      
## [31] "INCENP"    "NUSAP1"    "HIST1H2AH" "KNL1"      "KIF4A"     "ANLN"     
## [37] "HIST1H3F"  "RFC3"     
## 
## $brown
##  [1] "AFF3"      "DTHD1"     "SESTD1"    "PTPN3"     "MIR4422HG" "MYB"      
##  [7] "HAVCR2"    "PECAM1"    "LINC02320" "HAVCR1"    "MCTP2"     "UBE2E2"   
## [13] "LYST"      "TIGIT"    
## 
## $blue
##  [1] "RPS19"  "RPS2"   "CD52"   "IL32"   "RPL41"  "RPS16"  "CRIP1"  "FAU"   
##  [9] "LTB"    "TMSB10" "RPS15"  "S100A4" "ACTG1"  "GAPDH"  "RPS28"  "RPL23" 
## [17] "ACTB"   "RPS13"  "S100A6"
## 
## $yellow
##  [1] "ATP5PF"     "USP18"      "HLA-DQA2"   "AC017028.1" "INSL6"     
##  [6] "RHEBL1"     "MRPL20-AS1" "GOLIM4"     "AC004551.1" "CDT1"      
## [11] "HLA-DRB1"   "IFI6"       "C2orf92"    "TRIM21"    
## 
## [1] "Methadone"
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -1.7674
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.32024
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.9936e-30
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## Warning in irlba(A = t(x = object), nv = npcs, ...): You're computing too large
## a percentage of total singular values, use a standard svd instead.

## PC_ 1 
## Positive:  KIF11, TUBA1B, MND1, HIST1H2AH, MRPL18, CCNF, AURKB, EIF4A3, KIF23, UBE2C 
##     HIST1H2BD, PGAM1, CDCA2, KIF15, ARL2, CCNA2, HIST1H2BB, SKA1, HIST1H3G, HIST2H4B 
## Negative:  ANK3, LINC00278, BCL2, CWC25, SATB1-AS1, MGAT4A, EGLN3, CCR6, RALGPS2, ZBTB20 
##     LINC01876, TTC39C, ABAT, RETREG1, PRKCA, SLC25A13, CYTH3, TSPAN3, TANC2, SLC4A5 
## PC_ 2 
## Positive:  RPL13A, RPL19, RPS12, RPS23, RPL28, RPS18, RPLP2, RPS27, RPS17, RPS28 
##     RPS21, RPL9, RPS16, RPL37A, RPS15, RPL41, RPL23A, RPL18A, RPL36A, RPL35 
## Negative:  TBCEL, HDAC1, RORA, IFNAR2, INPP5F, GRAMD1B, DENND1A, SUCLA2, MAP2K6, NHEJ1 
##     KIF16B, RASA1, HECA, SERINC5, CAMKMT, RIPOR2, PHF21A, MARCH3, TCEANC2, SULT1B1 
## PC_ 3 
## Positive:  PSMB4, CDK1, HIST1H3G, CDCA8, CDC20, HIST1H2BB, JAKMIP1, DEPDC1B, CCNB1, CDON 
##     KIF23, UBE2C, CCNB2, HIST1H3B, CDCA2, ARL2, CCNA2, SKA1, HIST1H3F, PLK2 
## Negative:  FANCB, LIN52, ADD3-AS1, PXMP2, FANCA, HELLS, CSTF2, LINC00871, URB1, GPATCH4 
##     C15orf41, ATAD2, ZGRF1, BRIP1, CHROMR, CENPU, XRCC2, XYLB, POLE2, IPPK 
## PC_ 4 
## Positive:  RPL36A, ZNF177, TMSB10, RPL38, RPS15A, LYRM7, GAPDH, RPS2, MYL6, RPL18A 
##     RPL37A, TMSB4X, TESK2, KCNMB4, RPL41, PARK7, CIAO2A, DNM3, EEF1G, RPS24 
## Negative:  TTK, EFCAB5, TPX2, NCAPG, HJURP, STIL, KIF4A, E2F8, OGN, ASPM 
##     RAD51AP1, CENPA, KIF18B, AC003093.1, ERH, HIST1H2AL, CDCA5, P4HB, CDON, CCNB1 
## PC_ 5 
## Positive:  BCAS4, ZC3H12B, CCL28, TMEM72-AS1, UST, TXNDC12, SEC22C, RFESD, MAP3K7CL, SPIN3 
##     ACER3, DIRC3, IGSF9B, C5orf17, EPHA4, CLDN12, FHIT, RHBDD1, AC233976.1, LRRN3 
## Negative:  TCEANC2, ANTXR2, CLCN3, SEPTIN8, RRM2B, GDAP1, AUTS2, CNDP2, SAMD3, AC107223.1 
##     AL162493.1, GABPB1, POMK, AL080250.1, AL138778.1, DDX10, TP63, B4GALT5, TNFRSF19, HOMER2 
##    Power SFT.R.sq   slope truncated.R.sq mean.k. median.k. max.k.
## 1      1 2.69e-01  4.8700         0.8230  143.00   143.000  162.0
## 2      2 9.82e-02  1.5000         0.4690   81.60    79.900  105.0
## 3      3 2.73e-05 -0.0141         0.1190   48.80    46.300   73.2
## 4      4 1.13e-01 -0.6200         0.0367   30.80    28.200   55.1
## 5      5 3.74e-01 -0.9590         0.2290   20.50    17.900   45.0
## 6      6 5.53e-01 -1.1400         0.4250   14.50    11.600   38.7
## 7      7 6.16e-01 -1.2600         0.5200   10.80     7.810   34.5
## 8      8 6.93e-01 -1.2600         0.6640    8.40     5.570   31.7
## 9      9 6.46e-01 -1.2600         0.6420    6.81     4.010   29.6
## 10    10 6.45e-01 -1.2100         0.6590    5.70     2.990   27.9
## 11    12 6.20e-01 -1.1300         0.7800    4.30     1.780   25.6
## 12    14 6.82e-01 -1.0800         0.8520    3.48     1.080   23.8
## 13    16 6.02e-01 -1.0600         0.7670    2.94     0.678   22.5
## 14    18 6.99e-01 -0.9930         0.8560    2.57     0.441   21.3
## 15    20 6.46e-01 -0.9690         0.8030    2.29     0.291   20.3

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##  0  1  2  3  4  5  6  7  8  9 
## 44 48 37 34 22 19 18 16 15 11

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 10 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 9 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 9 module eigengenes in given set.

## $turquoise
##  [1] "KIF11"     "TUBA1B"    "MND1"      "HIST1H2AH" "MRPL18"    "CCNF"     
##  [7] "AURKB"     "EIF4A3"    "KIF23"     "UBE2C"     "HIST1H2BD" "PGAM1"    
## [13] "CDCA2"     "KIF15"     "ARL2"      "CCNA2"     "HIST1H2BB" "SKA1"     
## [19] "HIST1H3G"  "HIST2H4B"  "CDK1"      "HMMR"      "PLK2"      "TMEM60"   
## [25] "HIST1H2AM" "PSMB4"     "CDCA8"     "CDC20"     "JAKMIP1"   "DEPDC1B"  
## [31] "CCNB1"     "CDON"      "CCNB2"     "HIST1H3B"  "HIST1H3F"  "C21orf58" 
## [37] "CCDC34"    "TTK"       "TPX2"      "NCAPG"     "HJURP"     "ASPM"     
## [43] "RAD51AP1"  "CENPA"     "KIF18B"    "HIST1H2AL" "P4HB"      "NCAPH"    
## 
## $brown
##  [1] "ANK3"       "BCL2"       "RALGPS2"    "ZBTB20"     "RETREG1"   
##  [6] "PRKCA"      "CYTH3"      "TANC2"      "FOXP1"      "KIF16B"    
## [11] "MARCH3"     "BCAS4"      "ZC3H12B"    "CCL28"      "TMEM72-AS1"
## [16] "UST"        "TXNDC12"    "SEC22C"     "RFESD"      "MAP3K7CL"  
## [21] "SPIN3"      "DIRC3"      "IGSF9B"     "C5orf17"    "EPHA4"     
## [26] "CLDN12"     "FHIT"       "RHBDD1"     "AC233976.1" "LRRN3"     
## [31] "LEF1-AS1"   "ADAM22"     "HS1BP3"     "AC092650.1"
## 
## $black
##  [1] "MGAT4A"  "TBCEL"   "RORA"    "INPP5F"  "GRAMD1B" "SUCLA2"  "RASA1"  
##  [8] "HECA"    "SERINC5" "CAMKMT"  "RIPOR2"  "PHF21A"  "R3HDM1"  "TXK"    
## [15] "MIATNB"  "DPP8"   
## 
## $blue
##  [1] "RPL13A"     "RPL19"      "RPS12"      "RPS23"      "RPL28"     
##  [6] "RPS18"      "RPLP2"      "RPS27"      "RPS17"      "RPS28"     
## [11] "RPS21"      "RPL9"       "RPS16"      "RPL37A"     "RPS15"     
## [16] "RPL41"      "RPL23A"     "RPL18A"     "RPL36A"     "RPL35"     
## [21] "RACK1"      "RPS24"      "SERF2"      "ACTG1"      "TMSB10"    
## [26] "RPL38"      "RPS15A"     "GAPDH"      "RPS2"       "MYL6"      
## [31] "TMSB4X"     "PARK7"      "EEF1G"      "LTB"        "AC079793.1"
## [36] "RPL11"      "RPL23"     
## 
## $magenta
##  [1] "RPS4X"     "FANCA"     "CSTF2"     "LINC00871" "C15orf41"  "XRCC2"    
##  [7] "DPF3"      "TESK2"     "HDGF"      "STAM"      "CD109"    
## 
## $yellow
##  [1] "NHEJ1"      "TCEANC2"    "CLCN3"      "AC073529.1" "ANTXR2"    
##  [6] "SEPTIN8"    "RRM2B"      "GDAP1"      "CNDP2"      "AC107223.1"
## [11] "AL162493.1" "POMK"       "AL080250.1" "AL138778.1" "TP63"      
## [16] "TNFRSF19"   "HOMER2"     "UTP25"      "AFG1L"      "AC022893.1"
## [21] "SLC19A2"    "ALDH3A2"   
## 
## $green
##  [1] "FANCB"      "LIN52"      "ADD3-AS1"   "PXMP2"      "HELLS"     
##  [6] "URB1"       "ATAD2"      "ZGRF1"      "BRIP1"      "CHROMR"    
## [11] "CENPU"      "XYLB"       "NT5DC3"     "ZNF519"     "DNA2"      
## [16] "EFCAB5"     "STIL"       "KIF4A"      "E2F8"       "OGN"       
## [21] "AC003093.1" "ERH"        "CDCA5"      "DDX10"      "PHF7"      
## [26] "MPLKIP"     "CYP7B1"     "CDK14"      "RAB33B"     "GINS4"     
## [31] "AC104806.2" "CARNMT1"    "CYSLTR1"    "HLF"       
## 
## $red
##  [1] "GPATCH4"    "IPPK"       "FADD"       "LIX1L-AS1"  "SUCLG2-AS1"
##  [6] "SHMT2"      "NSMCE1"     "PRDX4"      "SCN8A"      "PRMT1"     
## [11] "PRDX2"      "FOSL2"      "AOAH"       "PTPN22"     "MAP3K9"    
## [16] "GSTP1"      "UBE2T"      "IL5RA"     
## 
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "23/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "469/10000 permutations failed the Mann-Whitney test."
## [1] "56/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $turquoise
##  [1] "KIF11"     "TUBA1B"    "MND1"      "HIST1H2AH" "MRPL18"    "CCNF"     
##  [7] "AURKB"     "EIF4A3"    "KIF23"     "UBE2C"     "HIST1H2BD" "PGAM1"    
## [13] "CDCA2"     "KIF15"     "ARL2"      "CCNA2"     "HIST1H2BB" "SKA1"     
## [19] "HIST1H3G"  "HIST2H4B"  "CDK1"      "HMMR"      "PLK2"      "TMEM60"   
## [25] "HIST1H2AM" "PSMB4"     "CDCA8"     "CDC20"     "JAKMIP1"   "DEPDC1B"  
## [31] "CCNB1"     "CDON"      "CCNB2"     "HIST1H3B"  "HIST1H3F"  "C21orf58" 
## [37] "CCDC34"    "TTK"       "TPX2"      "NCAPG"     "HJURP"     "ASPM"     
## [43] "RAD51AP1"  "CENPA"     "KIF18B"    "HIST1H2AL" "P4HB"      "NCAPH"    
## 
## $brown
##  [1] "ANK3"       "BCL2"       "RALGPS2"    "ZBTB20"     "RETREG1"   
##  [6] "PRKCA"      "CYTH3"      "TANC2"      "FOXP1"      "KIF16B"    
## [11] "MARCH3"     "BCAS4"      "ZC3H12B"    "CCL28"      "TMEM72-AS1"
## [16] "UST"        "TXNDC12"    "SEC22C"     "RFESD"      "MAP3K7CL"  
## [21] "SPIN3"      "DIRC3"      "IGSF9B"     "C5orf17"    "EPHA4"     
## [26] "CLDN12"     "FHIT"       "RHBDD1"     "AC233976.1" "LRRN3"     
## [31] "LEF1-AS1"   "ADAM22"     "HS1BP3"     "AC092650.1"
## 
## $black
##  [1] "MGAT4A"  "TBCEL"   "RORA"    "INPP5F"  "GRAMD1B" "SUCLA2"  "RASA1"  
##  [8] "HECA"    "SERINC5" "CAMKMT"  "RIPOR2"  "PHF21A"  "R3HDM1"  "TXK"    
## [15] "MIATNB"  "DPP8"   
## 
## $blue
##  [1] "RPL13A"     "RPL19"      "RPS12"      "RPS23"      "RPL28"     
##  [6] "RPS18"      "RPLP2"      "RPS27"      "RPS17"      "RPS28"     
## [11] "RPS21"      "RPL9"       "RPS16"      "RPL37A"     "RPS15"     
## [16] "RPL41"      "RPL23A"     "RPL18A"     "RPL36A"     "RPL35"     
## [21] "RACK1"      "RPS24"      "SERF2"      "ACTG1"      "TMSB10"    
## [26] "RPL38"      "RPS15A"     "GAPDH"      "RPS2"       "MYL6"      
## [31] "TMSB4X"     "PARK7"      "EEF1G"      "LTB"        "AC079793.1"
## [36] "RPL11"      "RPL23"     
## 
## $magenta
##  [1] "RPS4X"     "FANCA"     "CSTF2"     "LINC00871" "C15orf41"  "XRCC2"    
##  [7] "DPF3"      "TESK2"     "HDGF"      "STAM"      "CD109"    
## 
## $yellow
##  [1] "NHEJ1"      "TCEANC2"    "CLCN3"      "AC073529.1" "ANTXR2"    
##  [6] "SEPTIN8"    "RRM2B"      "GDAP1"      "CNDP2"      "AC107223.1"
## [11] "AL162493.1" "POMK"       "AL080250.1" "AL138778.1" "TP63"      
## [16] "TNFRSF19"   "HOMER2"     "UTP25"      "AFG1L"      "AC022893.1"
## [21] "SLC19A2"    "ALDH3A2"   
## 
## $green
##  [1] "FANCB"      "LIN52"      "ADD3-AS1"   "PXMP2"      "HELLS"     
##  [6] "URB1"       "ATAD2"      "ZGRF1"      "BRIP1"      "CHROMR"    
## [11] "CENPU"      "XYLB"       "NT5DC3"     "ZNF519"     "DNA2"      
## [16] "EFCAB5"     "STIL"       "KIF4A"      "E2F8"       "OGN"       
## [21] "AC003093.1" "ERH"        "CDCA5"      "DDX10"      "PHF7"      
## [26] "MPLKIP"     "CYP7B1"     "CDK14"      "RAB33B"     "GINS4"     
## [31] "AC104806.2" "CARNMT1"    "CYSLTR1"    "HLF"       
## 
## $red
##  [1] "GPATCH4"    "IPPK"       "FADD"       "LIX1L-AS1"  "SUCLG2-AS1"
##  [6] "SHMT2"      "NSMCE1"     "PRDX4"      "SCN8A"      "PRMT1"     
## [11] "PRDX2"      "FOSL2"      "AOAH"       "PTPN22"     "MAP3K9"    
## [16] "GSTP1"      "UBE2T"      "IL5RA"
saveRDS(mods2, "~/gibbs/DOGMAMORPH/Ranalysis/modules/20230529ProliferatingModules_Treatment.rds")

#finally looking at all proliferating cells to see if we can find something interesting, just got 2 out of it
mods3<-ModID(results, nPCS = 9, softpower = 6)
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.4183
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.30103
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 9.8548e-16
## PC_ 1 
## Positive:  ANK3, TSHZ2, ZBTB20, FAAH2, MAML2, PRKCA, LDLRAD4, PCAT1, ABLIM1, TTN 
##     MGAT4A, C22orf34, UST, AL136456.1, PFKFB3, TAFA1, SESN3, MPP7, LINC01422, AL353660.1 
## Negative:  TUBA1B, TUBB, HIST1H4C, GAPDH, RRM2, STMN1, DIAPH3, ACTB, PFN1, HIST1H3B 
##     POLQ, TYMS, NCAPG, TK1, HIST1H2AH, TMPO, PCLAF, HIST1H1B, CFL1, HMGN2 
## PC_ 2 
## Positive:  POLQ, NCAPG, DIAPH3, SPC25, CIT, KIF18B, KIF15, RRM2, ASPM, ATAD5 
##     NCAPG2, CDCA2, NUSAP1, KIF11, KIF14, TOP2A, KNL1, BUB1B, KIF4A, BRIP1 
## Negative:  RPL28, RPL18A, RPL41, RPS15, RPL27A, RPL13A, RPS28, RPS19, RPL11, RPS12 
##     RPS23, RPS29, RPS18, RPS27, RPL10, RPL18, RPL37, RPS16, B2M, RPLP1 
## PC_ 3 
## Positive:  ABLIM1, ZBTB20, MGAT5, MAP3K1, RORA, WDFY2, SSBP2, MAP3K4, RFX3, MCF2L2 
##     TSHZ2, ARL15, AL136456.1, DUSP16, AKT3, ATP13A3, PHF21A, UST, MAST4, PRKCA 
## Negative:  MTRNR2L8, NKG7, AGAP1, PECAM1, CCL5, GZMA, MKI67, CD8A, CENPF, HMGB2 
##     KLRK1, CD8B, AOAH, ZEB2, KPNA2, NAALADL2, TOP2A, HIST1H1E, HSP90B1, INCENP 
## PC_ 4 
## Positive:  PTPN3, MIR4422HG, PECAM1, DTHD1, LYST, SESTD1, GZMK, NCOA1, MCTP2, CNR2 
##     HAVCR2, AL031599.1, UBE2E2, AGAP1, AFF3, KLRK1, ANTXR2, TRPS1, SAMD3, RPTOR 
## Negative:  LTB, SORL1, MAP3K1, ANK3, TTC39C, KIF14, TSHZ2, CDCA2, KIF4A, CKAP2L 
##     KIF2C, TNFAIP3, CDCA8, JUNB, UBE2C, ESPL1, RPS19, EPHA4, FMN1, SGO2 
## PC_ 5 
## Positive:  DTL, MSH6, CLSPN, TRERF1, EXO1, CDC45, FANCA, MCM4, CDC6, CCNE2 
##     CTSW, HELLS, CCL5, ZEB2, POLE2, MCOLN2, C1orf21, MTHFD1L, FAM111B, THEMIS 
## Negative:  SESN3, SESTD1, MIR4422HG, KIF14, PTPN3, LDLRAD4, PLK1, KIF20A, KIF23, AFF3 
##     KIF4A, HMMR, BACH2, AURKB, TXK, DTHD1, CCNB2, APOLD1, AURKA, CDCA8 
##    Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1      1  0.00548 -0.71          0.359 174.000  1.73e+02 194.00
## 2      2  0.31800 -2.72          0.415  93.800  9.08e+01 120.00
## 3      3  0.56700 -2.90          0.564  51.700  4.81e+01  77.10
## 4      4  0.68100 -2.40          0.666  29.200  2.55e+01  51.90
## 5      5  0.63700 -2.34          0.611  17.000  1.38e+01  36.40
## 6      6  0.69700 -2.04          0.660  10.200  7.62e+00  26.40
## 7      7  0.67700 -1.88          0.651   6.380  4.18e+00  19.70
## 8      8  0.68000 -1.70          0.635   4.120  2.32e+00  15.10
## 9      9  0.22600 -3.56          0.120   2.750  1.30e+00  11.70
## 10    10  0.22600 -3.15          0.132   1.900  7.36e-01   9.26
## 11    12  0.21700 -2.64          0.131   0.986  2.50e-01   5.97
## 12    14  0.21100 -2.31          0.120   0.557  8.78e-02   3.98
## 13    16  0.21300 -2.17          0.119   0.335  3.52e-02   2.72
## 14    18  0.79800 -1.11          0.782   0.210  1.38e-02   1.89
## 15    20  0.78800 -1.07          0.746   0.135  5.59e-03   1.33

## TOM calculation: adjacency..
## ..will not use multithreading.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

## dynamicMods
##   0   1   2   3   4   5   6   7   8 
## 135  48  37  31  24  19  14  12  11

##  mergeCloseModules: Merging modules whose distance is less than 0.5
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 9 module eigengenes in given set.
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.
##    Calculating new MEs...
##    multiSetMEs: Calculating module MEs.
##      Working on set 1 ...
##      moduleEigengenes: Calculating 5 module eigengenes in given set.

## $red
##  [1] "TSHZ2"      "ABLIM1"     "AL136456.1" "LINC01876"  "MGAT5"     
##  [6] "RORA"       "MAP3K4"     "DUSP16"     "PHF21A"     "MAST4"     
## [11] "NEAT1"      "CDHR3"      "AL589693.1" "PLCL1"     
## 
## $yellow
##  [1] "PCAT1"      "AGAP1"      "PECAM1"     "PTPN3"      "MIR4422HG" 
##  [6] "DTHD1"      "LYST"       "SESTD1"     "GZMK"       "NCOA1"     
## [11] "MCTP2"      "CNR2"       "HAVCR2"     "AL031599.1" "UBE2E2"    
## [16] "AFF3"       "ANTXR2"     "TRPS1"      "SAMD3"      "AC104078.2"
## [21] "MYB"        "GFOD1"      "KCNQ5"      "CD38"      
## 
## $brown
##   [1] "TUBA1B"      "TUBB"        "HIST1H4C"    "RRM2"        "STMN1"      
##   [6] "DIAPH3"      "HIST1H3B"    "POLQ"        "NCAPG"       "HIST1H2AH"  
##  [11] "TMPO"        "PCLAF"       "HIST1H1B"    "PCNA"        "FBXO5"      
##  [16] "ASPM"        "SPC25"       "CIT"         "KIF18B"      "KIF15"      
##  [21] "ATAD5"       "NCAPG2"      "CDCA2"       "NUSAP1"      "KIF11"      
##  [26] "KIF14"       "TOP2A"       "KNL1"        "BUB1B"       "KIF4A"      
##  [31] "BRIP1"       "CIP2A"       "BRCA2"       "ECT2"        "FANCI"      
##  [36] "MKI67"       "ATP13A3"     "CENPF"       "HMGB2"       "KPNA2"      
##  [41] "HIST1H1E"    "HSP90B1"     "INCENP"      "HSP90AA1"    "CKAP2L"     
##  [46] "KIF2C"       "CDCA8"       "UBE2C"       "ESPL1"       "SGO2"       
##  [51] "KIF23"       "PLK1"        "CCNF"        "DTL"         "MSH6"       
##  [56] "CLSPN"       "EXO1"        "CDC45"       "FANCA"       "MCM4"       
##  [61] "CDC6"        "CCNE2"       "HELLS"       "POLE2"       "MTHFD1L"    
##  [66] "FAM111B"     "MPP6"        "HNRNPAB"     "CENPP"       "FANCC"      
##  [71] "KIF20A"      "HMMR"        "AURKB"       "CCNB2"       "APOLD1"     
##  [76] "AURKA"       "CENPA"       "CCNB1"       "SCMH1"       "C12orf75"   
##  [81] "DMC1"        "MCM5"        "FEN1"        "MCM7"        "MCM10"      
##  [86] "RRM1"        "MIR4435-2HG" "LGMN"        "IL2RA"       "KNTC1"      
##  [91] "F5"          "ADTRP"       "SELL"        "KHDC1"       "HIST1H3G"   
##  [96] "HIST1H3F"    "HIST1H2BH"   "HIST1H3D"    "CHTF18"      "HIST1H2BF"  
## [101] "HIST1H2AL"   "CKS1B"       "HIST1H2AI"   "HIST1H2AG"   "HIST2H4B"   
## [106] "HIST1H2BB"   "HIST1H3C"    "SBF2"        "CENPS"      
## 
## $black
##  [1] "GAPDH"      "ACTB"       "PFN1"       "CFL1"       "ACTG1"     
##  [6] "RPL28"      "RPL18A"     "RPL41"      "RPS15"      "RPL27A"    
## [11] "RPL13A"     "RPS28"      "RPS19"      "RPL11"      "RPS12"     
## [16] "RPS23"      "RPS29"      "RPS18"      "RPS27"      "RPL10"     
## [21] "RPL18"      "RPL37"      "RPS16"      "B2M"        "RPLP1"     
## [26] "RPS2"       "RPS27A"     "RPL37A"     "RPS15A"     "RPLP2"     
## [31] "PTMA"       "LTB"        "JUNB"       "SCD5"       "SPON1"     
## [36] "ANXA2"      "DAD1"       "AC022075.1" "NDUFA6"     "FKBP1A"    
## [41] "PKM"        "BCAT1"      "FABP5"      "NUTF2"      "LSM5"      
## [46] "PRDX1"      "ATP5F1E"    "TMSB10"     "RPS24"     
## 
## [1] "9485/10000 permutations failed the Mann-Whitney test."
## [1] "5647/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $brown
##   [1] "TUBA1B"      "TUBB"        "HIST1H4C"    "RRM2"        "STMN1"      
##   [6] "DIAPH3"      "HIST1H3B"    "POLQ"        "NCAPG"       "HIST1H2AH"  
##  [11] "TMPO"        "PCLAF"       "HIST1H1B"    "PCNA"        "FBXO5"      
##  [16] "ASPM"        "SPC25"       "CIT"         "KIF18B"      "KIF15"      
##  [21] "ATAD5"       "NCAPG2"      "CDCA2"       "NUSAP1"      "KIF11"      
##  [26] "KIF14"       "TOP2A"       "KNL1"        "BUB1B"       "KIF4A"      
##  [31] "BRIP1"       "CIP2A"       "BRCA2"       "ECT2"        "FANCI"      
##  [36] "MKI67"       "ATP13A3"     "CENPF"       "HMGB2"       "KPNA2"      
##  [41] "HIST1H1E"    "HSP90B1"     "INCENP"      "HSP90AA1"    "CKAP2L"     
##  [46] "KIF2C"       "CDCA8"       "UBE2C"       "ESPL1"       "SGO2"       
##  [51] "KIF23"       "PLK1"        "CCNF"        "DTL"         "MSH6"       
##  [56] "CLSPN"       "EXO1"        "CDC45"       "FANCA"       "MCM4"       
##  [61] "CDC6"        "CCNE2"       "HELLS"       "POLE2"       "MTHFD1L"    
##  [66] "FAM111B"     "MPP6"        "HNRNPAB"     "CENPP"       "FANCC"      
##  [71] "KIF20A"      "HMMR"        "AURKB"       "CCNB2"       "APOLD1"     
##  [76] "AURKA"       "CENPA"       "CCNB1"       "SCMH1"       "C12orf75"   
##  [81] "DMC1"        "MCM5"        "FEN1"        "MCM7"        "MCM10"      
##  [86] "RRM1"        "MIR4435-2HG" "LGMN"        "IL2RA"       "KNTC1"      
##  [91] "F5"          "ADTRP"       "SELL"        "KHDC1"       "HIST1H3G"   
##  [96] "HIST1H3F"    "HIST1H2BH"   "HIST1H3D"    "CHTF18"      "HIST1H2BF"  
## [101] "HIST1H2AL"   "CKS1B"       "HIST1H2AI"   "HIST1H2AG"   "HIST2H4B"   
## [106] "HIST1H2BB"   "HIST1H3C"    "SBF2"        "CENPS"      
## 
## $black
##  [1] "GAPDH"      "ACTB"       "PFN1"       "CFL1"       "ACTG1"     
##  [6] "RPL28"      "RPL18A"     "RPL41"      "RPS15"      "RPL27A"    
## [11] "RPL13A"     "RPS28"      "RPS19"      "RPL11"      "RPS12"     
## [16] "RPS23"      "RPS29"      "RPS18"      "RPS27"      "RPL10"     
## [21] "RPL18"      "RPL37"      "RPS16"      "B2M"        "RPLP1"     
## [26] "RPS2"       "RPS27A"     "RPL37A"     "RPS15A"     "RPLP2"     
## [31] "PTMA"       "LTB"        "JUNB"       "SCD5"       "SPON1"     
## [36] "ANXA2"      "DAD1"       "AC022075.1" "NDUFA6"     "FKBP1A"    
## [41] "PKM"        "BCAT1"      "FABP5"      "NUTF2"      "LSM5"      
## [46] "PRDX1"      "ATP5F1E"    "TMSB10"     "RPS24"
saveRDS(mods3, "~/gibbs/DOGMAMORPH/Ranalysis/modules/20230529ProliferatingModules.rds")

#in these cases, it doesnt make a lot of sense to go through and merge modules based on similarity. We're trying to preserve differences, so we may want to be able to preserve these separations even if things end up harder to analyze in the short term 
devtools::session_info()
## Warning in system("timedatectl", intern = TRUE): running command 'timedatectl'
## had status 1
## - Session info ---------------------------------------------------------------
##  setting  value
##  version  R version 4.2.0 (2022-04-22)
##  os       Red Hat Enterprise Linux 8.7 (Ootpa)
##  system   x86_64, linux-gnu
##  ui       X11
##  language (EN)
##  collate  C
##  ctype    C
##  tz       Etc/UTC
##  date     2023-05-31
##  pandoc   2.17.1.1 @ /usr/lib/rstudio-server/bin/quarto/bin/ (via rmarkdown)
## 
## - Packages -------------------------------------------------------------------
##  package          * version   date (UTC) lib source
##  abind              1.4-5     2016-07-21 [2] CRAN (R 4.2.0)
##  AnnotationDbi      1.60.2    2023-03-10 [1] Bioconductor
##  backports          1.4.1     2021-12-13 [2] CRAN (R 4.2.0)
##  base64enc          0.1-3     2015-07-28 [2] CRAN (R 4.2.0)
##  Biobase            2.58.0    2022-11-01 [1] Bioconductor
##  BiocGenerics       0.44.0    2022-11-01 [1] Bioconductor
##  BiocParallel       1.32.6    2023-03-17 [1] Bioconductor
##  Biostrings         2.66.0    2022-11-01 [1] Bioconductor
##  bit                4.0.5     2022-11-15 [2] CRAN (R 4.2.0)
##  bit64              4.0.5     2020-08-30 [2] CRAN (R 4.2.0)
##  bitops             1.0-7     2021-04-24 [2] CRAN (R 4.2.0)
##  blob               1.2.4     2023-03-17 [1] CRAN (R 4.2.0)
##  bslib              0.4.2     2022-12-16 [1] CRAN (R 4.2.0)
##  cachem             1.0.8     2023-05-01 [1] CRAN (R 4.2.0)
##  callr              3.7.3     2022-11-02 [1] CRAN (R 4.2.0)
##  checkmate          2.1.0     2022-04-21 [2] CRAN (R 4.2.0)
##  cli                3.6.1     2023-03-23 [1] CRAN (R 4.2.0)
##  cluster            2.1.4     2022-08-22 [2] CRAN (R 4.2.0)
##  codetools          0.2-19    2023-02-01 [2] CRAN (R 4.2.0)
##  colorspace         2.1-0     2023-01-23 [2] CRAN (R 4.2.0)
##  cowplot          * 1.1.1     2020-12-30 [2] CRAN (R 4.2.0)
##  crayon             1.5.2     2022-09-29 [2] CRAN (R 4.2.0)
##  data.table         1.14.8    2023-02-17 [2] CRAN (R 4.2.0)
##  DBI                1.1.3     2022-06-18 [2] CRAN (R 4.2.0)
##  deldir             1.0-6     2021-10-23 [2] CRAN (R 4.2.0)
##  devtools           2.4.5     2022-10-11 [1] CRAN (R 4.2.0)
##  digest             0.6.31    2022-12-11 [2] CRAN (R 4.2.0)
##  doParallel       * 1.0.17    2022-02-07 [1] CRAN (R 4.2.0)
##  dplyr            * 1.1.2     2023-04-20 [1] CRAN (R 4.2.0)
##  dynamicTreeCut   * 1.63-1    2016-03-11 [2] CRAN (R 4.2.0)
##  ellipsis           0.3.2     2021-04-29 [2] CRAN (R 4.2.0)
##  evaluate           0.20      2023-01-17 [2] CRAN (R 4.2.0)
##  fansi              1.0.4     2023-01-22 [2] CRAN (R 4.2.0)
##  fastcluster      * 1.2.3     2021-05-24 [2] CRAN (R 4.2.0)
##  fastmap            1.1.1     2023-02-24 [1] CRAN (R 4.2.0)
##  fastmatch          1.1-3     2021-07-23 [2] CRAN (R 4.2.0)
##  fitdistrplus       1.1-8     2022-03-10 [2] CRAN (R 4.2.0)
##  flashClust       * 1.01-2    2012-08-21 [1] CRAN (R 4.2.0)
##  foreach          * 1.5.2     2022-02-02 [2] CRAN (R 4.2.0)
##  foreign            0.8-84    2022-12-06 [2] CRAN (R 4.2.0)
##  Formula            1.2-5     2023-02-24 [1] CRAN (R 4.2.0)
##  fs                 1.6.1     2023-02-06 [2] CRAN (R 4.2.0)
##  future             1.32.0    2023-03-07 [1] CRAN (R 4.2.0)
##  future.apply       1.10.0    2022-11-05 [1] CRAN (R 4.2.0)
##  generics           0.1.3     2022-07-05 [2] CRAN (R 4.2.0)
##  GenomeInfoDb       1.34.9    2023-02-02 [1] Bioconductor
##  GenomeInfoDbData   1.2.9     2023-03-17 [1] Bioconductor
##  GenomicRanges      1.50.2    2022-12-16 [1] Bioconductor
##  ggplot2          * 3.4.2     2023-04-03 [1] CRAN (R 4.2.0)
##  ggrepel            0.9.3     2023-02-03 [1] CRAN (R 4.2.0)
##  ggridges           0.5.4     2022-09-26 [1] CRAN (R 4.2.0)
##  globals            0.16.2    2022-11-21 [1] CRAN (R 4.2.0)
##  glue               1.6.2     2022-02-24 [2] CRAN (R 4.2.0)
##  GO.db              3.16.0    2023-03-17 [1] Bioconductor
##  goftest            1.2-3     2021-10-07 [2] CRAN (R 4.2.0)
##  gridExtra          2.3       2017-09-09 [2] CRAN (R 4.2.0)
##  gtable             0.3.3     2023-03-21 [1] CRAN (R 4.2.0)
##  highr              0.10      2022-12-22 [1] CRAN (R 4.2.0)
##  Hmisc            * 5.1-0     2023-05-08 [1] CRAN (R 4.2.0)
##  htmlTable          2.4.1     2022-07-07 [1] CRAN (R 4.2.0)
##  htmltools          0.5.5     2023-03-23 [1] CRAN (R 4.2.0)
##  htmlwidgets        1.6.2     2023-03-17 [1] CRAN (R 4.2.0)
##  httpuv             1.6.9     2023-02-14 [1] CRAN (R 4.2.0)
##  httr               1.4.5     2023-02-24 [1] CRAN (R 4.2.0)
##  ica                1.0-3     2022-07-08 [2] CRAN (R 4.2.0)
##  igraph             1.4.2     2023-04-07 [1] CRAN (R 4.2.0)
##  impute             1.72.3    2023-01-19 [1] Bioconductor
##  IRanges            2.32.0    2022-11-01 [1] Bioconductor
##  irlba              2.3.5.1   2022-10-03 [1] CRAN (R 4.2.0)
##  iterators        * 1.0.14    2022-02-05 [2] CRAN (R 4.2.0)
##  jquerylib          0.1.4     2021-04-26 [2] CRAN (R 4.2.0)
##  jsonlite           1.8.4     2022-12-06 [2] CRAN (R 4.2.0)
##  KEGGREST           1.38.0    2022-11-01 [1] Bioconductor
##  KernSmooth         2.23-20   2021-05-03 [2] CRAN (R 4.2.0)
##  knitr              1.42      2023-01-25 [1] CRAN (R 4.2.0)
##  later              1.3.0     2021-08-18 [2] CRAN (R 4.2.0)
##  lattice            0.21-8    2023-04-05 [1] CRAN (R 4.2.0)
##  lazyeval           0.2.2     2019-03-15 [2] CRAN (R 4.2.0)
##  leiden             0.4.3     2022-09-10 [1] CRAN (R 4.2.0)
##  lifecycle          1.0.3     2022-10-07 [1] CRAN (R 4.2.0)
##  listenv            0.9.0     2022-12-16 [2] CRAN (R 4.2.0)
##  lmtest             0.9-40    2022-03-21 [2] CRAN (R 4.2.0)
##  magrittr           2.0.3     2022-03-30 [2] CRAN (R 4.2.0)
##  MASS               7.3-59    2023-04-21 [1] CRAN (R 4.2.0)
##  Matrix             1.5-4     2023-04-04 [1] CRAN (R 4.2.0)
##  matrixStats        0.63.0    2022-11-18 [2] CRAN (R 4.2.0)
##  memoise            2.0.1     2021-11-26 [2] CRAN (R 4.2.0)
##  mime               0.12      2021-09-28 [2] CRAN (R 4.2.0)
##  miniUI             0.1.1.1   2018-05-18 [2] CRAN (R 4.2.0)
##  munsell            0.5.0     2018-06-12 [2] CRAN (R 4.2.0)
##  nlme               3.1-162   2023-01-31 [1] CRAN (R 4.2.0)
##  nnet               7.3-19    2023-05-03 [1] CRAN (R 4.2.0)
##  openxlsx         * 4.2.5.2   2023-02-06 [1] CRAN (R 4.2.0)
##  parallelly         1.35.0    2023-03-23 [1] CRAN (R 4.2.0)
##  patchwork          1.1.2     2022-08-19 [1] CRAN (R 4.2.0)
##  pbapply            1.7-0     2023-01-13 [1] CRAN (R 4.2.0)
##  pillar             1.9.0     2023-03-22 [1] CRAN (R 4.2.0)
##  pkgbuild           1.4.0     2022-11-27 [1] CRAN (R 4.2.0)
##  pkgconfig          2.0.3     2019-09-22 [2] CRAN (R 4.2.0)
##  pkgload            1.3.2     2022-11-16 [1] CRAN (R 4.2.0)
##  plotly             4.10.1    2022-11-07 [1] CRAN (R 4.2.0)
##  plyr               1.8.8     2022-11-11 [1] CRAN (R 4.2.0)
##  png                0.1-8     2022-11-29 [1] CRAN (R 4.2.0)
##  polyclip           1.10-4    2022-10-20 [1] CRAN (R 4.2.0)
##  preprocessCore     1.60.2    2023-01-19 [1] Bioconductor
##  prettyunits        1.1.1     2020-01-24 [2] CRAN (R 4.2.0)
##  processx           3.8.1     2023-04-18 [1] CRAN (R 4.2.0)
##  profvis            0.3.8     2023-05-02 [1] CRAN (R 4.2.0)
##  progressr          0.13.0    2023-01-10 [1] CRAN (R 4.2.0)
##  promises           1.2.0.1   2021-02-11 [2] CRAN (R 4.2.0)
##  ps                 1.7.5     2023-04-18 [1] CRAN (R 4.2.0)
##  purrr              1.0.1     2023-01-10 [1] CRAN (R 4.2.0)
##  R6                 2.5.1     2021-08-19 [2] CRAN (R 4.2.0)
##  RANN               2.6.1     2019-01-08 [2] CRAN (R 4.2.0)
##  RColorBrewer       1.1-3     2022-04-03 [2] CRAN (R 4.2.0)
##  Rcpp               1.0.10    2023-01-22 [1] CRAN (R 4.2.0)
##  RcppAnnoy          0.0.20    2022-10-27 [1] CRAN (R 4.2.0)
##  RcppRoll           0.3.0     2018-06-05 [2] CRAN (R 4.2.0)
##  RCurl              1.98-1.12 2023-03-27 [1] CRAN (R 4.2.0)
##  remotes            2.4.2     2021-11-30 [2] CRAN (R 4.2.0)
##  reshape2           1.4.4     2020-04-09 [2] CRAN (R 4.2.0)
##  reticulate         1.28      2023-01-27 [1] CRAN (R 4.2.0)
##  rlang              1.1.1     2023-04-28 [1] CRAN (R 4.2.0)
##  rmarkdown          2.21      2023-03-26 [1] CRAN (R 4.2.0)
##  ROCR               1.0-11    2020-05-02 [2] CRAN (R 4.2.0)
##  rpart              4.1.19    2022-10-21 [1] CRAN (R 4.2.0)
##  Rsamtools          2.14.0    2022-11-01 [1] Bioconductor
##  RSQLite            2.3.1     2023-04-03 [1] CRAN (R 4.2.0)
##  rstudioapi         0.14      2022-08-22 [1] CRAN (R 4.2.0)
##  Rtsne              0.16      2022-04-17 [2] CRAN (R 4.2.0)
##  S4Vectors          0.36.2    2023-02-26 [1] Bioconductor
##  sass               0.4.5     2023-01-24 [1] CRAN (R 4.2.0)
##  scales             1.2.1     2022-08-20 [1] CRAN (R 4.2.0)
##  scattermore        0.8       2022-02-14 [1] CRAN (R 4.2.0)
##  sctransform        0.3.5     2022-09-21 [1] CRAN (R 4.2.0)
##  sessioninfo        1.2.2     2021-12-06 [2] CRAN (R 4.2.0)
##  Seurat           * 4.3.0     2022-11-18 [1] CRAN (R 4.2.0)
##  SeuratObject     * 4.1.3     2022-11-07 [1] CRAN (R 4.2.0)
##  shiny              1.7.4     2022-12-15 [1] CRAN (R 4.2.0)
##  Signac           * 1.9.0     2022-12-08 [1] CRAN (R 4.2.0)
##  sp                 1.6-0     2023-01-19 [1] CRAN (R 4.2.0)
##  spatstat.data      3.0-1     2023-03-12 [1] CRAN (R 4.2.0)
##  spatstat.explore   3.1-0     2023-03-14 [1] CRAN (R 4.2.0)
##  spatstat.geom      3.1-0     2023-03-12 [1] CRAN (R 4.2.0)
##  spatstat.random    3.1-4     2023-03-13 [1] CRAN (R 4.2.0)
##  spatstat.sparse    3.0-1     2023-03-12 [1] CRAN (R 4.2.0)
##  spatstat.utils     3.0-2     2023-03-11 [1] CRAN (R 4.2.0)
##  stringi            1.7.12    2023-01-11 [1] CRAN (R 4.2.0)
##  stringr            1.5.0     2022-12-02 [1] CRAN (R 4.2.0)
##  survival           3.5-5     2023-03-12 [1] CRAN (R 4.2.0)
##  tensor             1.5       2012-05-05 [2] CRAN (R 4.2.0)
##  tibble             3.2.1     2023-03-20 [1] CRAN (R 4.2.0)
##  tidyr              1.3.0     2023-01-24 [1] CRAN (R 4.2.0)
##  tidyselect         1.2.0     2022-10-10 [1] CRAN (R 4.2.0)
##  urlchecker         1.0.1     2021-11-30 [1] CRAN (R 4.2.0)
##  usethis            2.1.6     2022-05-25 [1] CRAN (R 4.2.0)
##  utf8               1.2.3     2023-01-31 [1] CRAN (R 4.2.0)
##  uwot               0.1.14    2022-08-22 [1] CRAN (R 4.2.0)
##  vctrs              0.6.2     2023-04-19 [1] CRAN (R 4.2.0)
##  viridisLite        0.4.2     2023-05-02 [1] CRAN (R 4.2.0)
##  WGCNA            * 1.72-1    2023-01-18 [1] CRAN (R 4.2.0)
##  withr              2.5.0     2022-03-03 [2] CRAN (R 4.2.0)
##  xfun               0.39      2023-04-20 [1] CRAN (R 4.2.0)
##  xtable             1.8-4     2019-04-21 [2] CRAN (R 4.2.0)
##  XVector            0.38.0    2022-11-01 [1] Bioconductor
##  yaml               2.3.7     2023-01-23 [1] CRAN (R 4.2.0)
##  zip                2.3.0     2023-04-17 [1] CRAN (R 4.2.0)
##  zlibbioc           1.44.0    2022-11-01 [1] Bioconductor
##  zoo                1.8-12    2023-04-13 [1] CRAN (R 4.2.0)
## 
##  [1] /gpfs/gibbs/project/ya-chi_ho/jac369/R/4.2
##  [2] /vast/palmer/apps/avx2/software/R/4.2.0-foss-2020b/lib64/R/library
## 
## ------------------------------------------------------------------------------